Annelise E. Barron is the W.M. Keck Associate Professor of Bioengineering at Stanford University.
The overall theme of the Barron lab is the study and biomimicry of natural host defense peptides (antimicrobial peptides). We study the molecular biophysics and mechanisms of LL-37—a centrally important human host defense peptide—and its involvement in Alzheimer's dementia (via LL-37 dysregulation and degradation by pathogen virulence factors). Alzheimer's dementia can be caused by (or at least, can be accompanied by) cerebral infections, a phenomenon now receiving renewed attention given recent discoveries. We are also working to develop biostable mimics of LL-37 as therapeutics that can combat antibiotic-resistant infections. Finally, we are working to mimic lung surfactant proteins that can facilitate the delivery of therapeutics to the lungs, treat bacterial and viral pneumonia, or prevent or treat ventilator-associated acute lung injury.
Dr. Barron was trained as a chemical engineer at the University of Washington (B.S.) and U.C. Berkeley (Ph.D.), and was a Pharmaceutical Chemistry postdoc with Prof. Ken A. Dill (UCSF) and Dr. Ronald N. Zuckermann (Chiron Corp.). She has served on the faculty at Stanford since 2007, and prior to that, served on the Chemical & Biological Engineering faculty of Northwestern University in Evanston, IL for 10 years (1997-2007). Dr. Barron has been awarded the Presidential Early Career Award for Scientists & Engineers (PECASE), the Beckman Young Investigator Award, and the Camille Dreyfus Teacher-Scholar Award, among other awards. Dr. Barron was the youngest scientist ever to serve on the Scientific Advisory Committee to the Director of the NIH, under Dr. Elias Zerhouni. She has more than 167 publications and a current H-index of 45 (Web of Science, All Databases), and serves on the advisory boards of several biotechnology companies.
Honors & Awards
National Hispanic Scholar, Univ. of Washington, Seattle (1986)
Tektronix Foundation Merit Scholarship, Univ. of Washington, Seattle (1986)
1986-1990 National Merit Scholar and Recipient of Associated Four-Year Scholarship, National Merit Scholarship Corporation (1986-1990)
University of Washington Undergraduate Merit Scholarship (two consecutive years), Univ. of Washington, Seattle (1988, 1989)
H.K. Benson Chemical Engineering Tuition Scholarship, Univ. of Washington, Seattle (1989)
1990-1993 U.C. Berkeley Chancellor's Minority Pre-doctoral Fellowship, U.C. Berkeley (1990-1993)
Outstanding Graduate Student Instructor Award, U.C. Berkeley Dept. of Chemical Engineering, U.C. Berkeley (1993)
U.C. Berkeley Provost's Research Fund Grant, U.C. Berkeley (1993)
Dow Excellence in Teaching Award, 1994, U.C. Berkeley Department of Chemical Engineering, U.C. Berkeley (1994)
Matheson Fellowship in Chemical Engineering, U.C. Berkeley (1994)
University of California Minority Dissertation Year Fellowship, U.C. Berkeley (1994)
NIH National Research Service Award (Postdoctoral Fellowship #1 F32 GM 18112), National Institutes of Health (1996)
Beckman Young Investigator Award, Arnold & Mabel Beckman Foundation (1998-99)
Presidential Early Career Award for Scientists and Engineers, NIH/NHGRI (1999)
Camille Dreyfus Teacher-Scholar Award, Camille and Henry Dreyfus Foundation (2002)
DuPont Young Professor Award, DuPont, Inc. (2002)
Thiele Lecturer in Chemical Engineering, University of Notre Dame (2005)
W.M. Keck Associate Professor of Bioengineering, Stanford University (2007-present)
Nanobio Scholar, Virginia Tech (2011)
Invited Participant, 2015 Nobel Symposium: Amyloid: A multifaceted player in human health and disease, Stockholm (June 10-11, 2015)
Invited Lecturer, Molecular Foundry, Lawrence Berkeley National Laboratory (March 6, 2018)
Invited Kornis Family Lecturer in Medicinal Chemistry, University of New South Wales, Department of Chemistry, Sydney, Australia (September 2019)
Postdoc, UCSF/Chiron Corporation, Biomimetic & Bioorganic Chemistry (1997)
Postdoc, Soane BioSciences/ACLARA Biosciences Inc., Molecular Biotechnology (1996)
Ph.D., Univ. of California, Berkeley, Chemical Engineering (1995)
B.S., Univ. of Washington, Seattle, Chemical Engineering (1990)
Current Research and Scholarly Interests
According to our recent findings, innate immune responses in humans and other mammals involving infection-, injury-, or stress-related dynamic imbalances between particular, immunomodulatory host defense peptides we study, and pro-amyloid / fibrillogenic peptides including ABeta and IAPP, may play a role in the poorly understood etiology of chronic / progressive plaque diseases, including diabetes type II melittus, atherosclerosis and Alzheimers dementia. All of these diseases involve senescent/dystrophic cells, inflammation, and proteopathies with plaque accumulation; and can be complicated by infection.
The latter disease, Alzheimers, is in need of a major breakthrough in fundamental understanding, more than almost any human disease currently under study. Of a total of 420+ clinical trials initiated by Pharma towards the development of Alzheimer's treatments over the past 15+ years, all of these trials have failed. There is no current effective treatment. Obviously, the most fundamental ideas for what drives Alzheimers must be flawed or incomplete.
Until recently Alzheimers disease was believed to be the sixth leading cause of death in the United States, according to the Centers for Disease Control and Prevention (CDC). But in March 2014, new research published in Neurology suggested that Alzheimers may actually be responsible for as many deaths each year as heart disease or cancer – the two leading causes of death in the U.S. – due to issues, in hospitals, of improper prior determinations of underlying cause of death in the elderly.
My lab is testing novel mechanistic hypotheses of Alzheimers etiology, based on recent, unique molecular biophysical observations of pro-amyloid and innate immune peptides. We are also looking at linkages to certain chronic infections.
Increasing numbers of epidemiological and co-morbidity studies indicate that multiple, progressive degenerative diseases, all involving plaque deposition in various body compartments, are linked. For instance, some researchers have begun to refer to Alzheimers Disease as "Diabetes Melittus Type III". We seek, with current projects, to sleuth out the shared molecular biophysical bases for these emerging linkages.
(Note: Succinct, exemplary summaries of these fascinating epidemiological / comorbidity linkages are found, for instance, in the following papers: "The ‘psoriatic march’: a concept of how severe psoriasis may drive cardiovascular comorbidity", Experimental Dermatology (2011) 20, 303–307; "Circle of Willis atherosclerosis: association with Alzheimer’s disease, neuritic plaques and neurofibrillary tangles", Acta Neuropathol (2007) 113:13–21; "Increased prevalence of the metabolic syndrome in patients with moderate to severe psoriasis", Arch Dermatol Res (2006) 298: 321–328; "Association of Alzheimer disease pathology with abnormal lipid metabolism", Neurology (2011) 77;1068).
- Advances in Biotechnology
BIOE 450, CHEMENG 450 (Spr)
- Biophysical Mechanisms of Innate Immunity
BIOE 236 (Win)
Independent Studies (5)
- Bioengineering Problems and Experimental Investigation
BIOE 191 (Win, Spr, Sum)
- Directed Investigation
BIOE 392 (Win, Spr, Sum)
- Directed Reading in Biophysics
BIOPHYS 399 (Aut, Win, Spr, Sum)
- Directed Study
BIOE 391 (Win, Spr, Sum)
- Graduate Research
BIOPHYS 300 (Aut, Win, Spr, Sum)
- Bioengineering Problems and Experimental Investigation
Prior Year Courses
- Advances in Biotechnology
BIOE 450, CHEMENG 450 (Spr)
- Advances in Biotechnology
The human cathelicidin LL-37 is a nanomolar inhibitor of amyloid self-assembly of islet amyloid polypeptide (IAPP).
Angewandte Chemie (International ed. in English)
Amyloid self-assembly of islet amyloid polypeptide (IAPP) is linked to pancreatic inflammation, β-cell degeneration, and the pathogenesis of type 2 diabetes (T2D). The multifunctional host defence peptides (HDPs) cathelicidins play crucial roles in inflammation. Here we show that the antimicrobial and immunomodu-latory polypeptide human cathelicidin LL-37 binds IAPP with nano-molar affinity and effectively suppresses its amyloid self-assembly and related pancreatic β-cell damage in vitro. In addition, we identify key LL-37 segments mediating its interaction with IAPP. Our results suggest a possible protective role for LL-37 in T2D pathogenesis and offer a molecular basis for the design of LL-37-derived peptides combining antimicrobial, immunomodulatory, and T2D-related anti-amyloid functions as promising candidates for multifunc-tional drugs.
View details for DOI 10.1002/anie.202000148
View details for PubMedID 31999880
Targeting Infectious Agents as a Therapeutic Strategy in Alzheimer’s Disease
View details for DOI 10.1007/s40263-020-00737-1
Optimizing Exogenous Surfactant as a Pulmonary Delivery Vehicle for Chicken Cathelicidin-2.
2020; 10 (1): 9392
The rising incidence of antibiotic-resistant lung infections has instigated a much-needed search for new therapeutic strategies. One proposed strategy is the use of exogenous surfactants to deliver antimicrobial peptides (AMPs), like CATH-2, to infected regions of the lung. CATH-2 can kill bacteria through a diverse range of antibacterial pathways and exogenous surfactant can improve pulmonary drug distribution. Unfortunately, mixing AMPs with commercially available exogenous surfactants has been shown to negatively impact their antimicrobial function. It was hypothesized that the phosphatidylglycerol component of surfactant was inhibiting AMP function and that an exogenous surfactant, with a reduced phosphatidylglycerol composition would increase peptide mediated killing at a distal site. To better understand how surfactant lipids interacted with CATH-2 and affected its function, isothermal titration calorimetry and solid-state nuclear magnetic resonance spectroscopy as well as bacterial killing curves against Pseudomonas aeruginosa were utilized. Additionally, the wet bridge transfer system was used to evaluate surfactant spreading and peptide transport. Phosphatidylglycerol was the only surfactant lipid to significantly inhibit CATH-2 function, showing a stronger electrostatic interaction with the peptide than other lipids. Although diluting the phosphatidylglycerol content in an existing surfactant, through the addition of other lipids, significantly improved peptide function and distal killing, it also reduced surfactant spreading. A synthetic phosphatidylglycerol-free surfactant however, was shown to further improve CATH-2 delivery and function at a remote site. Based on these in vitro experiments synthetic phosphatidylglycerol-free surfactants seem optimal for delivering AMPs to the lung.
View details for DOI 10.1038/s41598-020-66448-1
View details for PubMedID 32523049
Helical side chain chemistry of a peptoid-based SP-C analogue: Balancing structural rigidity and biomimicry.
Surfactant protein C (SP-C) is an important constituent of lung surfactant (LS) and, along with SP-B, is included in exogenous surfactant replacement therapies for treating respiratory distress syndrome (RDS). SP-C's biophysical activity depends upon the presence of a rigid C-terminal helix, of which the secondary structure is more crucial to functionality than precise side-chain chemistry. SP-C is highly sequence-conserved, suggesting that the beta-branched, aliphatic side chains of the helix are also important. Nonnatural mimics of SP-C were created using a poly-N-substituted glycine, or "peptoid," backbone. The mimics included varying amounts of alpha-chiral, aliphatic side chains and alpha-chiral, aromatic side chains in the helical region, imparting either biomimicry or structural rigidity. Biophysical studies confirmed that the peptoids mimicked SP-C's secondary structure and replicated many of its surface-active characteristics. Surface activity was optimized by incorporating both structurally rigid and biomimetic side chain chemistries in the helical region indicating that both characteristics are important for activity. By balancing these features in one mimic, a novel analogue was created that emulates SP-C's in vitro surface activity while overcoming many of the challenges related to natural SP-C. Peptoid-based analogues hold great potential for use in a synthetic, biomimetic LS formulation for treating RDS.
View details for PubMedID 30972750
- Role of Microbes in the Development of Alzheimer's Disease: State of the Art - An International Symposium Presented at the 2017 IAGG Congress in San Francisco FRONTIERS IN GENETICS 2018; 9
Effective in vivo treatment of acute lung injury with helical, amphipathic peptoid mimics of pulmonary surfactant proteins
2018; 8: 6795
Acute lung injury (ALI) leads to progressive loss of breathing capacity and hypoxemia, as well as pulmonary surfactant dysfunction. ALI's pathogenesis and management are complex, and it is a significant cause of morbidity and mortality worldwide. Exogenous surfactant therapy, even for research purposes, is impractical for adults because of the high cost of current surfactant preparations. Prior in vitro work has shown that poly-N-substituted glycines (peptoids), in a biomimetic lipid mixture, emulate key biophysical activities of lung surfactant proteins B and C at the air-water interface. Here we report good in vivo efficacy of a peptoid-based surfactant, compared with extracted animal surfactant and a synthetic lipid formulation, in a rat model of lavage-induced ALI. Adult rats were subjected to whole-lung lavage followed by administration of surfactant formulations and monitoring of outcomes. Treatment with a surfactant protein C mimic formulation improved blood oxygenation, blood pH, shunt fraction, and peak inspiratory pressure to a greater degree than surfactant protein B mimic or combined formulations. All peptoid-enhanced treatment groups showed improved outcomes compared to synthetic lipids alone, and some formulations improved outcomes to a similar extent as animal-derived surfactant. Robust biophysical mimics of natural surfactant proteins may enable new medical research in ALI treatment.
View details for PubMedID 29717157
Evidence that the Human Innate Immune Peptide LL-37 may be a Binding Partner of Amyloid-β and Inhibitor of Fibril Assembly
Journal of Alzheimer's Disease
2017; 59 (4): 1213-1226
Identifying physiologically relevant binding partners of amyloid-β (Aβ) that modulate in vivo fibril formation may yield new insights into Alzheimer's disease (AD) etiology. Human cathelicidin peptide, LL-37, is an innate immune effector and modulator, ubiquitous in human tissues and expressed in myriad cell types.We present in vitro experimental evidence and discuss findings supporting a novel hypothesis that LL-37 binds to Aβ42 and can modulate Aβ fibril formation.Specific interactions between LL-37 and Aβ (with Aβ in different aggregation states, assessed by capillary electrophoresis) were demonstrated by surface plasmon resonance imaging (SPRi). Morphological and structural changes were investigated by transmission electron microscopy (TEM) and circular dichroism (CD) spectroscopy. Neuroinflammatory and cytotoxic effects of LL-37 alone, Aβ42 alone, and LL-37/Aβ complexes were evaluated in human microglia and neuroblastoma cell lines (SH-SY5Y).SPRi shows binding specificity between LL-37 and Aβ, while TEM shows that LL-37 inhibits Aβ42 fibril formation, particularly Aβ's ability to form long, straight fibrils characteristic of AD. CD reveals that LL-37 prevents Aβ42 from adopting its typical β-type secondary structure. Microglia-mediated toxicities of LL-37 and Aβ42 to neurons are greatly attenuated when the two peptides are co-incubated prior to addition. We discuss the complementary biophysical characteristics and AD-related biological activities of these two peptides.Based on this body of evidence, we propose that LL-37 and Aβ42 may be natural binding partners, which implies that balanced (or unbalanced) spatiotemporal expression of the two peptides could impact AD initiation and progression.
View details for DOI 10.3233/JAD-170223
View details for PubMedCentralID PMC5611894
Intracellular biomass flocculation as a key mechanism of rapid bacterial killing by cationic, amphipathic antimicrobial peptides and peptoids.
2017; 7 (1): 16718
Many organisms rely on antimicrobial peptides (AMPs) as a first line of defense against pathogens. In general, most AMPs are thought to kill bacteria by binding to and disrupting cell membranes. However, certain AMPs instead appear to inhibit biomacromolecule synthesis, while causing less membrane damage. Despite an unclear understanding of mechanism(s), there is considerable interest in mimicking AMPs with stable, synthetic molecules. Antimicrobial N-substituted glycine (peptoid) oligomers ("ampetoids") are structural, functional and mechanistic analogs of helical, cationic AMPs, which offer broad-spectrum antibacterial activity and better therapeutic potential than peptides. Here, we show through quantitative studies of membrane permeabilization, electron microscopy, and soft X-ray tomography that both AMPs and ampetoids trigger extensive and rapid non-specific aggregation of intracellular biomacromolecules that correlates with microbial death. We present data demonstrating that ampetoids are "fast killers", which rapidly aggregate bacterial ribosomes in vitro and in vivo. We suggest intracellular biomass flocculation is a key mechanism of killing for cationic, amphipathic AMPs, which may explain why most AMPs require micromolar concentrations for activity, show significant selectivity for killing bacteria over mammalian cells, and finally, why development of resistance to AMPs is less prevalent than developed resistance to conventional antibiotics.
View details for PubMedID 29196622
View details for PubMedCentralID PMC5711933
In Vivo, In Vitro, and In Silico Characterization of Peptoids as Antimicrobial Agents
2016; 11 (2): 1-17
View details for DOI 10.1371/journal.pone.0135961
Human antimicrobial peptide LL-37 induces glial-mediated neuroinflammation
2015; 94 (2): 130-141
LL-37 is the sole cathelicidin-derived antimicrobial peptide found in humans. It becomes active upon C-terminal cleavage of its inactive precursor hCAP18. In addition to antimicrobial action, it also functions as an innate immune system stimulant in many tissues of the body. Here we report that hCAP18 and LL-37 are expressed in all organs of the human body that were studied with the highest basic levels being expressed in the GI tract and the brain. Its expression and functional role in the central nerve system (CNS) has not previously been reported. We found increased expression of LL-37 in IFNγ-stimulated human astrocytes and their surrogate U373 cells, as well as in LPS/IFNγ-stimulated human microglia and their surrogate monocyte-derived THP-1 cells. We found that treatment of microglia, astrocytes, THP-1 cells and U373 cells with LL-37 induced secretion of the inflammatory cytokines IL-1β and IL-6; the chemokines IL-8 and CCL-2, and other materials toxic to human neuroblastoma SH-SY5Y cells. The mechanism of LL-37 stimulation involves activation of intracellular proinflammatory pathways involving phospho-P38 MAP kinase and phospho-NFκB proteins. We blocked the inflammatory stimulant action of LL-37 by removing it with an anti-LL-37 antibody. The inflammatory effect was also prevented by treatment with inhibitors of PKC, PI3K and MEK-1/2 as well as with the intracellular Ca(2+)-chelator, BAPTA-AM. This indicates involvement of these intracellular pathways. Our data suggest that LL-37, in addition to its established roles, may play a role in the chronic neuroinflammation which is observed in neurodegenerative diseases such as Alzheimer's and Parkinson's disease.
View details for DOI 10.1016/j.bcP.2015.02.003
View details for Web of Science ID 000351479500008
View details for PubMedID 25686659
Vipericidins: a novel family of cathelicidin-related peptides from the venom gland of South American pit vipers
2014; 46 (11): 2561-2571
Cathelicidins are phylogenetically ancient, pleiotropic host defense peptides-also called antimicrobial peptides (AMPs)-expressed in numerous life forms for innate immunity. Since even the jawless hagfish expresses cathelicidins, these genetically encoded host defense peptides are at least 400 million years old. More recently, cathelicidins with varying antipathogenic activities and cytotoxicities were discovered in the venoms of poisonous snakes; for these creatures, cathelicidins may also serve as weapons against prey and predators, as well as for innate immunity. We report herein the expression of orthologous cathelicidin genes in the venoms of four different South American pit vipers (Bothrops atrox, Bothrops lutzi, Crotalus durissus terrificus, and Lachesis muta rhombeata)-distant relatives of Asian cobras and kraits, previously shown to express cathelicidins-and an elapid, Pseudonaja textilis. We identified six novel, genetically encoded peptides: four from pit vipers, collectively named vipericidins, and two from the elapid. These new venom-derived cathelicidins exhibited potent killing activity against a number of bacterial strains (S. pyogenes, A. baumannii, E. faecalis, S. aureus, E. coli, K. pneumoniae, and P. aeruginosa), mostly with relatively less potent hemolysis, indicating their possible usefulness as lead structures for the development of new anti-infective agents. It is worth noting that these South American snake venom peptides are comparable in cytotoxicity (e.g., hemolysis) to human cathelicidin LL-37, and much lower than other membrane-active peptides such as mastoparan 7 and melittin from bee venom. Overall, the excellent bactericidal profile of vipericidins suggests they are a promising template for the development of broad-spectrum peptide antibiotics.
View details for DOI 10.1007/s00726-014-1801-4
View details for Web of Science ID 000343995600010
View details for PubMedID 25100358
A tunable silk-alginate hydrogel scaffold for stem cell culture and transplantation.
2014; 35 (12): 3736-3743
One of the major challenges in regenerative medicine is the ability to recreate the stem cell niche, which is defined by its signaling molecules, the creation of cytokine gradients, and the modulation of matrix stiffness. A wide range of scaffolds has been developed in order to recapitulate the stem cell niche, among them hydrogels. This paper reports the development of a new silk-alginate based hydrogel with a focus on stem cell culture. This biocomposite allows to fine tune its elasticity during cell culture, addressing the importance of mechanotransduction during stem cell differentiation. The silk-alginate scaffold promotes adherence of mouse embryonic stem cells and cell survival upon transplantation. In addition, it has tunable stiffness as function of the silk-alginate ratio and the concentration of crosslinker - a characteristic that is very hard to accomplish in current hydrogels. The hydrogel and the presented results represents key steps on the way of creating artificial stem cell niche, opening up new paths in regenerative medicine.
View details for DOI 10.1016/j.biomaterials.2014.01.029
View details for PubMedID 24484675
Learning from host-defense peptides: cationic, amphipathic peptoids with potent anticancer activity.
2014; 9 (2)
Cationic, amphipathic host defense peptides represent a promising group of agents to be developed for anticancer applications. Poly-N-substituted glycines, or peptoids, are a class of biostable, peptidomimetic scaffold that can display a great diversity of side chains in highly tunable sequences via facile solid-phase synthesis. Herein, we present a library of anti-proliferative peptoids that mimics the cationic, amphipathic structural feature of the host defense peptides and explore the relationships between the structure, anticancer activity and selectivity of these peptoids. Several peptoids are found to be potent against a broad range of cancer cell lines at low-micromolar concentrations including cancer cells with multidrug resistance (MDR), causing cytotoxicity in a concentration-dependent manner. They can penetrate into cells, but their cytotoxicity primarily involves plasma membrane perturbations. Furthermore, peptoid 1, the most potent peptoid synthesized, significantly inhibited tumor growth in a human breast cancer xenotransplantation model without any noticeable acute adverse effects in mice. Taken together, our work provided important structural information for designing host defense peptides or their mimics for anticancer applications. Several cationic, amphipathic peptoids are very attractive for further development due to their high solubility, stability against protease degradation, their broad, potent cytotoxicity against cancer cells and their ability to overcome multidrug resistance.
View details for DOI 10.1371/journal.pone.0090397
View details for PubMedID 24587350
View details for PubMedCentralID PMC3938723
The Incorporation of Extracellular Matrix Proteins in Protein Polymer Hydrogels to Improve Encapsulated Beta-cell Function.
Annals of clinical and laboratory science
2013; 43 (2): 111-121
Biomaterial encapsulation of islets has been proposed to improve the long-term success of islet transplantation by recreating a suitable microenvironment and enhancing cell-matrix interactions that affect cellular function. Protein polymer hydrogels previously showed promise as a biocompatible scaffold by maintaining high cell viability. Here, enzymatically-crosslinked protein polymers were used to investigate the effects of varying scaffold properties and of introducing ECM proteins on the viability and function of encapsulated MIN6 β-cells. Chemical and mechanical properties of the hydrogel were modified by altering the protein concentrations while collagen IV, fibronectin, and laminin were incorporated to reestablish cell-matrix interactions lost during cell isolation. Rheology indicated all hydrogels formed quickly, resulting in robust, elastic hydrogels with Young's moduli similar to soft tissue. All hydrogels tested supported both high MIN6 β-cell viability and function and have the potential to serve as an encapsulation platform for islet cell delivery in vivo.
View details for PubMedID 23694784
Encapsulation of protein microfiber networks supporting pancreatic islets.
Journal of biomedical materials research. Part A
2012; 100 (12): 3384-3391
Networks of discrete, genipin-crosslinked gelatin microfibers enveloping pancreatic islets were incorporated within barium alginate microcapsules. This novel technique enabled encapsulation of cellular aggregates in a spherical fibrous matrix <300 μm in diameter. Microfibers were produced by vortex-drawn extrusion within an alginate support matrix. Optimization culminated in a hydrated fiber diameter of 22.3 ± 0.4 μm, a significant reduction relative to that available through current gelatin microfiber spinning techniques, while making the process more reliable and less labor intensive. Microfibers were encapsulated at 40 vol % within 294 ± 4 μm 1.6% barium alginate microparticles by electrostatic-mediated dropwise extrusion. Pancreatic islets extracted from Sprague Dawley rats were encapsulated within the microparticles and analyzed over 21 days. Acridine orange and propidium iodide fluorescent viability staining and light microscopy indicated a significant increase in viability for islets within the fiber-embedded particles relative to fiber-free controls at days 7, 14, and 21. The fiber-embedded system also promoted cellular aggregate cohesion, reducing the incidence of dispersed islet morphologies within the capsules from 31 to 8% at day 21. Further enquiry into benefits of islet encapsulation within a protein fiber network will be the subject of future investigation.
View details for DOI 10.1002/jbm.a.34281
View details for PubMedID 22767501
Enhanced function of pancreatic islets co-encapsulated with ECM proteins and mesenchymal stromal cells in a silk hydrogel
2012; 33 (28): 6691-6697
Pancreatic islet encapsulation within biosynthetic materials has had limited clinical success due to loss of islet function and cell death. As an alternative encapsulation material, a silk-based scaffold was developed to reestablish the islet microenvironment lost during cell isolation. Islets were encapsulated with ECM proteins (laminin and collagen IV) and mesenchymal stromal cells (MSCs), known to have immunomodulatory properties or to enhance islet cell graft survival and function. After a 7 day in vitro encapsulation, islets remained viable and maintained insulin secretion in response to glucose stimulation. Islets encapsulated with collagen IV, or laminin had increased insulin secretion at day 2 and day 7, respectively. A 3.2-fold synergistic improvement in islet insulin secretion was observed when islets were co-encapsulated with MSCs and ECM proteins. Furthermore, encapsulated islets had increased gene expression of functional genes; insulin I, insulin II, glucagon, somatostatin, and PDX-1, and lower expression of the de-differentiation genes cytokeratin 19 and vimentin compared to non-encapsulated cells. This work demonstrates that encapsulation in silk with both MSCs and ECM proteins enhances islet function and with further development may have potential as a suitable platform for islet delivery in vivo.
View details for DOI 10.1016/j.biomaterials.2012.06.015
View details for Web of Science ID 000308270000011
View details for PubMedID 22766242
- In Vivo Biodistribution and Small Animal PET of Cu-64-Labeled Antimicrobial Peptoids BIOCONJUGATE CHEMISTRY 2012; 23 (5): 1069-1079
Synthesis and Assembly of Functional High Molecular Weight Adiponectin Multimers in an Engineered Strain of Escherichia coil
2012; 13 (4): 1035-1042
Adiponectin has many beneficial effects on cardiovascular and obesity-related disorders. It is part of a class of proteins that contains short collagenous domains, along with surfactant proteins A and D, and complement protein C1q. This class of biomacromolecules requires post-translational modifications to form biologically active assemblies. By introducing a set of post-translational modifying enzymes into Escherichia coli , we have created a prokaryotic expression system that functionally assembles adiponectin, as assessed by the ability of produced adiponectin multimers to suppress human endothelial cell apoptosis. This study represents the first example of the assembly of functional high order multimers of any member of this class of proteins outside of eukaryotic cells. Furthermore, the results give fundamental insight into the process of assembly such as the necessity and sufficiency of various post-translational steps for functional assembly. We expect that fine-tuning of the expression system will allow for efficient production and functional assembly of biomolecules that assemble via short collagenous domains.
View details for DOI 10.1021/bm2017367
View details for Web of Science ID 000303076200010
View details for PubMedID 22376164
Antimicrobial Peptoids Are Effective against Pseudomonas aeruginosa Biofilms
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
2011; 55 (6): 3054-3057
The resistance of biofilms to conventional antibiotics complicates the treatment of chronic cystic fibrosis (CF). We investigated the effects of peptoids, peptides, and conventional antibiotics on the biomass and cell viability within Pseudomonas aeruginosa biofilms. At their MICs, peptoids 1 and 1-C13(4mer) caused maximum reductions in biomass and cell viability, respectively. These results suggest that peptoids of this class could be worth exploring for the treatment of pulmonary infections occurring in CF patients.
View details for DOI 10.1128/AAC.01516-10
View details for Web of Science ID 000290713400090
View details for PubMedID 21422218
View details for PubMedCentralID PMC3101385
Completely Monodisperse, Highly Repetitive Proteins for Bioconjugate Capillary Electrophoresis: Development and Characterization
2011; 12 (6): 2275-2284
Protein-based polymers are increasingly being used in biomaterial applications because of their ease of customization and potential monodispersity. These advantages make protein polymers excellent candidates for bioanalytical applications. Here we describe improved methods for producing drag-tags for free-solution conjugate electrophoresis (FSCE). FSCE utilizes a pure, monodisperse recombinant protein, tethered end-on to a ssDNA molecule, to enable DNA size separation in aqueous buffer. FSCE also provides a highly sensitive method to evaluate the polydispersity of a protein drag-tag and thus its suitability for bioanalytical uses. This method is able to detect slight differences in drag-tag charge or mass. We have devised an improved cloning, expression, and purification strategy that enables us to generate, for the first time, a truly monodisperse 20 kDa protein polymer and a nearly monodisperse 38 kDa protein. These newly produced proteins can be used as drag-tags to enable longer read DNA sequencing by free-solution microchannel electrophoresis.
View details for DOI 10.1021/bm200358r
View details for Web of Science ID 000291499900038
View details for PubMedID 21553840
View details for PubMedCentralID PMC3129339
Efficacy of Antimicrobial Peptoids against Mycobacterium tuberculosis
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
2011; 55 (6): 3058-3062
Tuberculosis is a leading cause of death worldwide. Resistance of Mycobacterium to antibiotics can make treatments less effective in some cases. We tested selected oligopeptoids--previously reported as mimics of natural host defense peptides--for activity against Mycobacterium tuberculosis and assessed their cytotoxicity. A tetrameric, alkylated, cationic peptoid (1-C13(4mer)) was most potent against M. tuberculosis and least cytotoxic, whereas an unalkylated analogue, peptoid 1(4mer), was inactive. Peptoid 1-C13(4mer) thus merits further study as a potential antituberculosis drug.
View details for DOI 10.1128/AAC.01667-10
View details for Web of Science ID 000290713400091
View details for PubMedID 21464254
View details for PubMedCentralID PMC3101442
Tunable, Post-translational Hydroxylation of Collagen Domains in Escherichia coli
ACS CHEMICAL BIOLOGY
2011; 6 (4): 320-324
Prolyl 4-hydroxylases are ascorbate-dependent oxygenases that play key roles in a variety of eukaryotic biological processes including oxygen sensing, siRNA regulation, and collagen folding. They perform their functions by catalyzing the post-translational hydroxylation of specific proline residues on target proteins to form (2S,4R)-4-hydroxyproline. Thus far, the study of these post-translational modifications has been limited by the lack of a prokaryotic recombinant expression system for producing hydroxylated proteins. By introducing a biosynthetic shunt to produce ascorbate-like molecules in Eschericia coli cells that heterologously express human prolyl 4-hydroxylase (P4H), we have created a strain of E. coli that produces collagenous proteins with high levels of (2S,4R)-4-hydroxyproline. Using this new system, we have observed hydroxylation patterns indicative of a processive catalytic mode for P4H that is active even in the absence of ascorbate. Our results provide insights into P4H enzymology and create a foundation for better understanding how post-translational hydroxylation affects proteins.
View details for DOI 10.1021/cb100298r
View details for Web of Science ID 000289455400005
View details for PubMedID 21210682
A 265-Base DNA Sequencing Read by Capillary Electrophoresis with No Separation Matrix
2011; 83 (2): 509-515
Electrophoretic DNA sequencing without a polymer matrix is currently possible only with the use of some kind of "drag-tag" as a mobility modifier. In free-solution conjugate electrophoresis (FSCE), a drag-tag attached to each DNA fragment breaks linear charge-to-friction scaling, enabling size-based separation in aqueous buffer alone. Here we report a 265-base read for free-solution DNA sequencing by capillary electrophoresis using a random-coil protein drag-tag of unprecedented length and purity. We identified certain methods of protein expression and purification that allow the production of highly monodisperse drag-tags as long as 516 amino acids, which are almost charge neutral (+1 to +6) and yet highly water-soluble. Using a four-color LIF detector, 265 bases could be read in 30 min with a 267-amino acid drag-tag, on par with the average read of current next-gen sequencing systems. New types of multichannel systems that allow much higher throughput electrophoretic sequencing should be much more accessible in the absence of a requirement for viscous separation matrix.
View details for DOI 10.1021/ac102188p
View details for Web of Science ID 000286129800007
View details for PubMedID 21182303
View details for PubMedCentralID PMC3271724
Protein Polymer MRI Contrast Agents: Longitudinal Analysis of Biomaterials In Vivo
MAGNETIC RESONANCE IN MEDICINE
2011; 65 (1): 220-228
Despite recent advances in tissue engineering to regenerate biological function by combining cells with material supports, development is hindered by inadequate techniques for characterizing biomaterials in vivo. Magnetic resonance imaging is a tomographic technique with high temporal and spatial resolution and represents an excellent imaging modality for longitudinal noninvasive assessment of biomaterials in vivo. To distinguish biomaterials from surrounding tissues for magnetic resonance imaging, protein polymer contrast agents were developed and incorporated into hydrogels. In vitro and in vivo images of protein polymer hydrogels, with and without covalently incorporated protein polymer contrast agents, were acquired by magnetic resonance imaging. T(1) values of the labeled gels were consistently lower when protein polymer contrast agents were included. As a result, the protein polymer contrast agent hydrogels facilitated fate tracking, quantification of degradation, and detection of immune response in vivo. For the duration of the in vivo study, the protein polymer contrast agent-containing hydrogels could be distinguished from adjacent tissues and from the foreign body response surrounding the gels. The hydrogels containing protein polymer contrast agent have a contrast-to-noise ratio 2-fold greater than hydrogels without protein polymer contrast agent. In the absence of the protein polymer contrast agent, hydrogels cannot be distinguished by the end of the gel lifetime.
View details for DOI 10.1002/mrm.22587
View details for Web of Science ID 000285963500025
View details for PubMedID 20740653
Short Alkylated Peptoid Mimics of Antimicrobial Lipopeptides
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
2011; 55 (1): 417-420
We report the creation of alkylated poly-N-substituted glycine (peptoid) mimics of antimicrobial lipopeptides with alkyl tails ranging from 5 to 13 carbons. In several cases, alkylation significantly improved the selectivity of the peptoids with no loss in antimicrobial potency. Using this technique, we synthesized an antimicrobial peptoid only 5 monomers in length with selective, broad-spectrum antimicrobial activity as potent as previously reported dodecameric peptoids and the antimicrobial peptide pexiganan.
View details for DOI 10.1128/AAC.01080-10
View details for Web of Science ID 000285577400059
View details for PubMedID 20956607
- Helical side chain chemistry of a peptoid-based SP-C analogue: Balancing structural rigidity and biomimicry BIOPOLYMERS 2019; 110 (6)
- Periprosthetic Bacterial Biofilm and Quorum Sensing JOURNAL OF ORTHOPAEDIC RESEARCH 2018; 36 (9): 2331–39
Evidence that the Human Innate Immune Peptide LL-37 May Be a Binding Partner of Abeta and Inhibitor of Fibril Assembly
CELL PRESS. 2018: 393A
View details for Web of Science ID 000430450000449
Effect of side chain hydrophobicity and cationic charge on antimicrobial activity and cytotoxicity of helical peptoids.
Bioorganic & medicinal chemistry letters
2018; 28 (2): 170–73
Peptoids are peptidomimetic polymers that are resistant to proteolysis and less prone to immune responses; thus, they can provide a practical alternative to peptides. Among the various therapeutic applications that have been explored, cationic amphipathic peptoids have demonstrated broad-spectrum antibacterial activity, including activity towards drug-resistant bacterial strains. While their potency and activity spectrum can be manipulated by sequence variations, bacterial selectivity and systemic toxicity need to be improved for further clinical development. To this aim, we incorporated various hydrophobic or cationic residues to improve the selectivity of the previously developed antibacterial peptoid 1. The analogs with hydrophobic residues demonstrated non-specific cytotoxicity, while those with an additional cationic residue showed improved selectivity and comparable antibacterial activity. Specifically, compared to 1, peptoid 7 showed much lower hemolysis and cytotoxicity, while maintaining the antibacterial activity. Therefore, we believe that peptoid 7 has the potential to serve as a promising alternative to current antimicrobial therapies.
View details for PubMedID 29198866
Implant-Associated Bacterial Biofilm and Quorum Sensing in Periprosthetic Joint Infections.
Journal of orthopaedic research : official publication of the Orthopaedic Research Society
Periprosthetic joint infection (PJI) continues to be a common complication after total knee arthroplasty and total hip arthroplasty leading to severe morbidity and mortality. With an aging population and increasing prevalence of total joint replacement procedures, the burden of PJI will be felt not only by individual patients, but in increased healthcare costs. Current treatment of PJI is inadequate resulting in incredibly high failure rates. This is believed to be largely mediated by the presence of bacterial biofilms. These polymicrobial bacterial colonies form within secreted extracellular matrices, adhering to the implant surface and local tissue. The biofilm architecture is believed to play a complex and critical role in a variety of bacterial processes including nutrient supplementation, metabolism, waste management, and antibiotic and immune resistance. The establishment of these biofilms relies heavily on the quorum sensing communication systems utilized by bacteria. Early stage research into disrupting bacterial communication by targeting quorum sensing show promise for future clinical applications. However, prevention of the biofilm formation via early forced induction of the biofilm forming process remains yet unexplored. This article is protected by copyright. All rights reserved.
View details for PubMedID 29663554
- In Vivo, In Vitro, and In Silico Characterization of Peptoids as Antimicrobial Agents PLOS ONE 2016; 11 (2)
Prostate tumor specific peptide-peptoid hybrid prodrugs
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
2015; 25 (14): 2849-2852
Inspired by naturally occurring host defense peptides, cationic amphipathic peptoids provide a promising scaffold for anti-cancer therapeutics. Herein, we report a library of peptide-peptoid hybrid prodrugs that can be selectively activated by prostate cancer cells. We have identified several compounds demonstrating potent anti-cancer activity with good to moderate selectivity. We believe that these prodrugs can provide a useful design principle for next generation peptide-peptoid hybrid prodrugs.
View details for DOI 10.1016/j.bmcl.2015.04.092
View details for Web of Science ID 000355663100024
View details for PubMedID 26022845
- No evidence of pathogenic involvement of cathelicidins in patient cohorts and mouse models of lupus and arthritis. PloS one 2014; 9 (12)
Protein polymer hydrogels: Effects of endotoxin on biocompatibility.
Journal of biomaterials applications
2013; 28 (3): 395-406
Protein polymer-based hydrogels have shown potential for tissue engineering applications, but require biocompatibility testing for in vivo use. Enzymatically crosslinked protein polymer-based hydrogels were tested in vitro and in vivo to evaluate their biocompatibility. Endotoxins present in the hydrogel were removed by Trition X-114 phase separation. The reduction of endotoxins decreased TNF-α production by a macrophage cell line in vitro; however, significant inflammatory response was still present compared to collagen control gels. A branched PEG molecule and dexamethasone were added to the hydrogel to reduce the response. In vitro testing showed a decrease in the TNF-α levels with the addition of dexamethasone. In vivo implantations into the epididymal fat pad of C57/BL6 mice, however, indicated a decreased inflammatory mediated immune response with a hydrogel treated with both PEGylation and endotoxin reduction. This study demonstrates the importance of endotoxin testing and removal in determining the biocompatibility of biomaterials.
View details for DOI 10.1177/0885328212454555
View details for PubMedID 22832218
A Readily Applicable Strategy to Convert Peptides to Peptoid-based Therapeutics
2013; 8 (3)
Incorporation of unnatural amino acids and peptidomimetic residues into therapeutic peptides is highly efficacious and commonly employed, but generally requires laborious trial-and-error approaches. Previously, we demonstrated that C20 peptide has the potential to be a potential antiviral agent. Herein we report our attempt to improve the biological properties of this peptide by introducing peptidomimetics. Through combined alanine, proline, and sarcosine scans coupled with a competitive fluorescence polarization assay developed for identifying antiviral peptides, we enabled to pinpoint peptoid-tolerant peptide residues within C20 peptide. The synergistic benefits of combining these (and other) commonly employed methods could lead to a easily applicable strategy for designing and refining therapeutically-attractive peptidomimetics.
View details for DOI 10.1371/journal.pone.0058874
View details for Web of Science ID 000316546400014
View details for PubMedID 23555603
View details for PubMedCentralID PMC3605428
- Encapsulation of protein microfiber networks supporting pancreatic islets JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A 2012; 100A (12): 3384-3391
Microfabricated devices for biomolecule encapsulation
2012; 33 (17): 2639-2649
Biomolecule encapsulation in droplets is important for miniaturizing biological assays to reduce reagent consumption, cost and time of analysis, and can be most effectively achieved by using microfabricated devices. Microfabricated fluidic devices can generate emulsified drops of uniform size with controlled dimensions and contents. Biological and chemical components such as cells, microgels, beads, hydrogel precursors, polymer initiators, and other droplets can be encapsulated within these drops. Encapsulated emulsions are appealing for a variety of applications since drops can be used as tiny reaction vessels to perform high-throughput reactions at fast rates, consuming minimal sample and solvent amounts due to the small size (micron diameters) of the emulsion drops. Facile mixing and droplet coalescence allow for a diversity of assays to be performed on-chip with tunable parameters. The simplicity of operation and speed of analysis with microencapsulated drops lends itself well to an array of quantitative biomolecular studies such as directed evolution, single-molecule DNA amplification, single-cell encapsulation, high-throughput sequencing, enzyme kinetics, and microfluidic cell culture. This review highlights recent advances in the field of microfabricated encapsulating devices, emphasizing the development of emulsifying encapsulations, device design, and current assays that are performed using encapsulating droplets.
View details for DOI 10.1002/elps.201200189
View details for Web of Science ID 000308581100004
View details for PubMedID 22965707
- A Four-Arm Star-Shaped Poly(ethylene glycol) (StarPEG) Platform for Bombesin Peptide Delivery to Gastrin-Releasing Peptide Receptors in Prostate Cancer ACS MACRO LETTERS 2012; 1 (6): 753-757
Alginate-PEG Sponge Architecture and Role in the Design of Insulin Release Dressings
2012; 13 (5): 1478-1485
Wound healing is a natural process involving several signaling molecules and cell types over a significant period of time. Although current dressings help to protect the wound from debris or infection, they do little in accelerating the healing process. Insulin has been shown to stimulate the healing of damaged skin. We have developed an alginate sponge dressing (ASD) that forms a hydrogel capable of providing a moist and protective healing environment. By incorporating insulin-loaded poly(d,l-lactide-co-glycolide) (PLGA) microparticles into ASD, we successfully stabilized and released insulin for up to 21 days. Insulin release and water absorption and transfer through the ASD were influenced by altering the levels of poly(ethylene glycol) (PEG) in the dressing matrix. Bioactivity of released insulin can be maintained for at least 10 days, demonstrated using a human keratinocyte migration assay. Results showed that insulin-loaded PLGA microparticles, embedded within PEG-ASD, functioned as an effective long-term delivery platform for bioactive insulin.
View details for DOI 10.1021/bm300186k
View details for Web of Science ID 000303951600028
View details for PubMedID 22506765
Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis
2012; 33 (3): 483-491
DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.
View details for DOI 10.1002/elps.201100452
View details for Web of Science ID 000299629800010
View details for PubMedID 22331820
View details for PubMedCentralID PMC3416024
In Vivo Biodistribution and Small Animal PET of (64)Cu-Labeled Antimicrobial Peptoids.
Peptoids are a rapidly developing class of biomimetic polymers based on oligo-N-substituted glycine backbones, designed to mimic peptides and proteins. Inspired by natural antimicrobial peptides, a group of cationic amphipathic peptoids has been successfully discovered with potent, broad-spectrum activity against pathogenic bacteria; however, there are limited studies to address the in vivo pharmacokinetics of the peptoids. Herein, (64)Cu-labeled DOTA conjugates of three different peptoids and two control peptides were synthesized and assayed in vivo by both biodistribution studies and small animal positron emission tomography (PET). The study was designed in a way to assess how structural differences of the peptidomimetics affect in vivo pharmacokinetics. As amphipathic molecules, major uptake of the peptoids occurred in the liver. Increased kidney uptake was observed by deleting one hydrophobic residue in the peptoid, and (64)Cu-3 achieved the highest kidney uptake of all the conjugates tested in this study. In comparison to peptides, our data indicated that peptoids had general in vivo properties of higher tissue accumulation, slower elimination, and higher in vivo stability. Different administration routes (intravenous, intraperitoneal, and oral) were investigated with peptoids. When administered orally, the peptoids showed poor bioavailability, reminiscent of that of peptide. However, remarkably longer passage through the gastrointestinal (GI) tract without rapid digestion was observed for peptoids. These unique in vivo properties of peptoids were rationalized by efficient cellular membrane permeability and protease resistance of peptoids. The results observed in the biodistribution studies could be confirmed by PET imaging, which provides a reliable way to evaluate in vivo pharmacokinetic properties of peptoids noninvasively and in real time. The pharmacokinetic data presented here can provide insight for further development of the antimicrobial peptoids as pharmaceuticals.
View details for PubMedID 22486390
View details for PubMedCentralID PMC3410980
Peptoid transporters: effects of cationic, amphipathic structure on their cellular uptake
2012; 8 (10): 2626-2628
Two cationic, amphipathic peptoids (poly-N-substituted glycines) were developed as new molecular transporters, which have extensive cellullar uptake and utilize different internalization mechanisms from purely cationic polyguanidine comparators.
View details for DOI 10.1039/c2mb25197c
View details for Web of Science ID 000308098600019
View details for PubMedID 22828784
View details for PubMedCentralID PMC3431920
Monodisperse, "Highly" Positively Charged Protein Polymer Drag-Tags Generated in an Intein-Mediated Purification System Used in Free-Solution Electrophoretic Separations of DNA
2012; 13 (1): 117-123
Free-solution conjugate electrophoresis (FSCE) is a method of DNA sequencing that eliminates the need for viscous polymer solutions by tethering a carefully designed, mobility modifying "drag-tag" to each DNA molecule to achieve size-based separations of DNA. The most successful drag-tags to date are genetically engineered, highly repetitive polypeptides ("protein polymers") that are designed to be large, water-soluble, and completely monodisperse. Positively charged arginines were deliberately introduced at regular intervals into the amino acid sequence to increase the hydrodynamic drag without increasing drag-tag length. Additionally, a one-step purification method that combines affinity chromatography and on-column tag cleavage was devised to achieve the required drag-tag monodispersity. Sequencing with a read length of approximately 180 bases was successfully achieved with a known sequence in free-solution electrophoresis using one of these positively charged drag-tags. This preliminary result is expected to lead to further progress in FSCE sequencing with ~400 bases read length possible when more "highly" positively charged protein polymers of larger size are generated with the intein system.
View details for DOI 10.1021/bm2013313
View details for Web of Science ID 000298897300013
View details for PubMedID 22168388
View details for PubMedCentralID PMC3270947
Ultrafast, efficient separations of large-sized dsDNA in a blended polymer matrix by microfluidic chip electrophoresis: A design of experiments approach
2011; 32 (22): 3233-3240
Double-stranded (ds) DNA fragments over a wide size range were successfully separated in blended polymer matrices by microfluidic chip electrophoresis. Novel blended polymer matrices composed of two types of polymers with three different molar masses were developed to provide improved separations of large dsDNA without negatively impacting the separation of small dsDNA. Hydroxyethyl celluloses with average molar masses of ∼27 kDa and ∼1 MDa were blended with a second class of polymer, high-molar mass (∼7 MDa) linear polyacrylamide. Fast and highly efficient separations of commercially available DNA ladders were achieved on a borosilicate glass microchip. A distinct separation of a 1-kb DNA extension ladder (200-40,000 bp) was completed in 2 min. An orthogonal design of experiments was used to optimize experimental parameters for DNA separations over a wide size range. We find that the two dominant factors are the applied electric field strength and the inclusion of a high concentration of low-molar mass polymer in the matrix solution. These two factors exerted different effects on the separations of small dsDNA fragments below 1 kbp, medium dsDNA fragments between 1 and 10 kbp, and large dsDNA fragments above 10 kbp.
View details for DOI 10.1002/elps.201100260
View details for Web of Science ID 000298098700020
View details for PubMedID 22009451
Blinded study determination of high sensitivity and specificity microchip electrophoresis-SSCP/HA to detect mutations in the p53 gene
2011; 32 (21): 2921-2929
Knowledge of the genetic changes that lead to disease has grown and continues to grow at a rapid pace. However, there is a need for clinical devices that can be used routinely to translate this knowledge into the treatment of patients. Use in a clinical setting requires high sensitivity and specificity (>97%) in order to prevent misdiagnoses. Single-strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are two DNA-based, complementary methods for mutation detection that are inexpensive and relatively easy to implement. However, both methods are most commonly detected by slab gel electrophoresis, which can be labor-intensive, time-consuming, and often the methods are unable to produce high sensitivity and specificity without the use of multiple analysis conditions. Here, we demonstrate the first blinded study using microchip electrophoresis (ME)-SSCP/HA. We demonstrate the ability of ME-SSCP/HA to detect with 98% sensitivity and specificity >100 samples from the p53 gene exons 5-9 in a blinded study in an analysis time of <10 min.
View details for DOI 10.1002/elps.201100396
View details for Web of Science ID 000298101000001
View details for PubMedID 22002021
View details for PubMedCentralID PMC3416029
Functional Synergy between Antimicrobial Peptoids and Peptides against Gram-Negative Bacteria
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
2011; 55 (11): 5399-5402
Antimicrobial peptides (AMPs) are integral components of innate immunity and are typically found in combinations in which they can synergize for broader-spectrum or more potent activity. Previously, we reported peptoid mimics of AMPs with potent and selective antimicrobial activity. Using checkerboard assays, we demonstrate that peptoids and AMPs can interact synergistically, with fractional inhibitory concentration indices as low as 0.16. These results strongly suggest that antimicrobial peptoids and peptides are functionally and mechanistically analogous.
View details for DOI 10.1128/AAC.00578-11
View details for Web of Science ID 000296375600069
View details for PubMedID 21859945
Biomimetic N-Terminal Alkylation of Peptoid Analogues of Surfactant Protein C
2011; 101 (5): 1076-1085
Surfactant protein C (SP-C) is a hydrophobic lipopeptide that is critical for lung function, in part because it physically catalyzes the formation of surface-associated surfactant reservoirs. Many of SP-C's key biophysical properties derive from its highly stable and hydrophobic α-helix. However, SP-C's posttranslational modification with N-terminal palmitoyl chains also seems to be quite important. We created a new (to our knowledge) class of variants of a synthetic, biomimetic family of peptide mimics (peptoids) that allow us to study the functional effects of biomimetic N-terminal alkylation in vitro. Mimics were designed to emulate the amphipathic patterning, helicity, and hydrophobicity of SP-C, and to include no, one, or two vicinal amide-linked, N-terminal octadecyl chains (providing a reach equivalent to that of natural palmitoyl chains). Pulsating bubble surfactometry and Langmuir-Wilhelmy surface balance studies showed that alkylation improved biomimetic surface activities, yielding lower film compressibility and lower maximum dynamic surface tensions. Atomic force microscopy studies indicated that alkyl chains bind to and retain segregated interfacial surfactant phases at low surface tensions by inducing 3D structural transitions in the monolayer's fluid-like phase, forming surfactant-associated reservoirs. Peptoid-based SP-C mimics are easily produced and purified, and offer much higher chemical and secondary structure stability than polypeptide-based mimics. In surfactant replacements intended for medical use, synthetic SP mimics reduce the odds of pathogen contamination, which may facilitate the wider use of surfactant treatment of respiratory disorders and diseases.
View details for DOI 10.1016/j.bpj.2011.04.055
View details for Web of Science ID 000294653800008
View details for PubMedID 21889444
- A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis (vol 687, pg 150, 2011) ANALYTICA CHIMICA ACTA 2011; 699 (1): 126-126
Peptoids: Bio-Inspired Polymers as Potential Pharmaceuticals
CURRENT PHARMACEUTICAL DESIGN
2011; 17 (25): 2732-2747
Peptoids are a developing class of peptide-like oligomers originally invented for drug discovery in the early 1990s. While peptides hold great promise for therapeutic applications, current development of peptide-based pharmaceuticals is hindered by their potential for misfolding and aggregation, and particularly, for rapid in vivo degradation post-administration. Researchers have investigated alternative peptide-like constructs that may be able to circumvent such complications. Peptoids comprise a peptide-based backbone and N-substituted glycines for side chain residues, resulting in complete protease-resistance. Synthesis of peptoid sequences up to 50 units in length allows for controlled sequence composition and incorporation of diverse side chain chemistries. Though the landscape of peptoid structure is not clearly defined, secondary, tertiary, loop, turn, and random structures have been identified. As protease-resistant isomers of peptides, peptoids are being developed as versatile molecular tools in biochemistry and biophysics, and are becoming attractive candidates for therapeutic and diagnostic applications. Peptoids have thus far demonstrated bioactivity as protein mimics and as replacements for small molecule drugs. In this review, we discuss the most recent advances in peptoid research on the therapeutic front in the last few years, including in vitro and in vivo studies in the fields of lung surfactant therapy, antimicrobial agents, diagnostics, and cancer. We particularly focus on the biophysical activity of lipid-associated peptoids and their potential therapeutic applications.
View details for Web of Science ID 000299629900013
View details for PubMedID 21728985
- Landscape of Next-Generation Sequencing Technologies ANALYTICAL CHEMISTRY 2011; 83 (12): 4327-4341
Non-ionic, thermo-responsive DEA/DMA nanogels: Synthesis, characterization, and use for DNA separations by microchip electrophoresis
JOURNAL OF COLLOID AND INTERFACE SCIENCE
2011; 357 (2): 345-353
Thermo-responsive polymer "nanogels" (crosslinked hydrogel particles with sub-100 nm diameters) are intriguing for many potential applications in biotechnology and medicine. There have been relatively few reports of electrostatically neutral, thermosensitive nanogels comprising a high fraction of hydrophilic co-monomer. Here we demonstrate the syntheses and characterization of novel, non-ionic nanogels based on random N,N-diethylacrylamide (DEA)/N,N-dimethylacrylamide (DMA) copolymers, made by free-radical, surfactant-free dispersion polymerization. The volume-phase transition temperatures of these DEA/DMA nanogels are strongly affected by co-monomer composition, providing a way to "tune" the phase transition temperature of these non-ionic nanogels. While DEA nanogels (comprising no DMA) can be obtained at 70 °C by standard emulsion precipitation, DEA/DMA random co-polymer nanogels can be obtained only in a particular range of temperatures, above the initial phase transition temperature and below the critical precipitation temperature of the DEA/DMA copolymer, controlled by co-monomer composition. Increasing percentages of DMA in the nanogels raises the phase transition temperature, and attenuates and broadens it as well. We find that concentrated DEA/DMA nanogel dispersions are optically clear at room temperature. This good optical clarity was exploited for their use in a novel DNA sieving matrix for microfluidic chip electrophoresis. An ultrafast, high-efficiency dsDNA separation was achieved in less than 120 s for dsDNA ranging from 75 bp to 15,000 bp.
View details for DOI 10.1016/j.jcis.2011.01.079
View details for Web of Science ID 000289179500013
View details for PubMedID 21392778
Free-solution electrophoretic separations of DNA-drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength
2011; 32 (10): 1201-1208
Here, we demonstrate the potential for high-resolution electrophoretic separations of ssDNA-protein conjugates in borosilicate glass microfluidic chips, with no sieving media and excellent repeatability. Using polynucleotides of two different lengths conjugated to moderately cationic protein polymer drag-tags, we measured separation efficiency as a function of applied electric field. In excellent agreement with prior theoretical predictions of Slater et al., resolution is found to remain constant as applied field is increased up to 700 V/cm, the highest field we were able to apply. This remarkable result illustrates the fundamentally different physical limitations of free-solution conjugate electrophoresis (FSCE)-based DNA separations relative to matrix-based DNA electrophoresis. ssDNA separations in "gels" have always shown rapidly declining resolution as the field strength is increased; this is especially true for ssDNA > 400 bases in length. FSCE's ability to decouple DNA peak resolution from applied electric field suggests the future possibility of ultra-rapid FSCE sequencing on chips. We investigated sources of peak broadening for FSCE separations on borosilicate glass microchips, using six different protein polymer drag-tags. For drag-tags with four or more positive charges, electrostatic and adsorptive interactions with poly(N-hydroxyethylacrylamide)-coated microchannel walls led to appreciable band-broadening, while much sharper peaks were seen for bioconjugates with nearly charge-neutral protein drag-tags.
View details for DOI 10.1002/elps.201000574
View details for Web of Science ID 000290586200014
View details for PubMedID 21500207
View details for PubMedCentralID PMC3416026
A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis
ANALYTICA CHIMICA ACTA
2011; 687 (2): 150-158
Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples.
View details for DOI 10.1016/j.aca.2010.12.016
View details for Web of Science ID 000287564700007
View details for PubMedID 21277417
A fluorescence polarization assay using an engineered human respiratory syncytial virus F protein as a direct screening platform
2011; 409 (2): 195-201
Human respiratory syncytial virus (hRSV) typically affects newborns and young children. Even though it can cause severe and, in some cases, lifelong respiratory infections, there are currently no Food and Drug Administration (FDA)-approved therapeutics that control this virus. The hRSV F protein facilitates viral fusion, a critical extracellular event that can be targeted for therapeutic intervention by disrupting the assembly of a postfusion 6-helix bundle (6HB) within the hRSV F protein. Here we report the development of a fluorescence polarization (FP) assay using an engineered hRSV F protein 5-helix bundle (5HB). We generated the 5HB and validated its ability to form a 6HB in an FP assay. To test the potential of 5HB as a screening tool, we then investigated a series of truncated peptides derived from the "missing" sixth helix. Using this FP-based 5HB system, we have successfully demonstrated that short peptides can prevent 6HB formation and serve as potential hRSV fusion inhibitors. We anticipate that this new 5HB system will provide an effective tool to identify and study potential antivirals to control hRSV infection.
View details for DOI 10.1016/j.ab.2010.10.020
View details for Web of Science ID 000287176600005
View details for PubMedID 20971054
View details for PubMedCentralID PMC3462168
- PROTEIN POLYMERS Gene libraries open up NATURE MATERIALS 2011; 10 (2): 83-84
Purification of HIV RNA from Serum Using a Polymer Capture Matrix in a Microfluidic Device
2011; 83 (3): 982-988
In this report, we demonstrate the purification of DNA and RNA from a 10% serum sample using an oligonucleotide capture matrix. This approach provides a one-stage, completely aqueous system capable of purifying both RNA and DNA for downstream PCR amplification. The advantages of utilizing the polymer capture matrix method in place of the solid-phase extraction method is that the capture matrix eliminates both guanidine and the 2-propanol wash that can inhibit downstream PCR and competition with proteins for the binding sites that can limit the capacity of the device. This method electrophoreses a biological sample (e.g., serum) containing the nucleic acid target through a polymer matrix with covalently bound oligonucleotides. These capture oligonucleotides selectively hybridize and retain the target nucleic acid, while the other biomolecules and reagents (e.g., SDS) pass through the matrix to waste. Following this purification step, the solution can be heated above the melting temperature of the capture sequence to release the target molecule, which is then electrophoresed to a recovery chamber for subsequent PCR amplification. We demonstrate that the device can be applied to purify both DNA and RNA from serum. The gag region of HIV at a starting concentration of 37.5 copies per microliter was successfully purified from a 10% serum sample demonstrating the applicability of this method to detect viruses present in low copy numbers.
View details for DOI 10.1021/ac102736g
View details for Web of Science ID 000286689600050
View details for PubMedID 21214255
View details for PubMedCentralID PMC3270936
Progress in the De Novo Design of Structured Peptoid Protein Mimics
2011; 96 (5): 556-560
Significant progress has been made in recent years toward creating interesting, unique, and in some cases, predictable oligopeptoid/polypeptoid secondary, tertiary, and in one case, quaternary structures. This article describes this progress, identifies a few of the many remaining challenges, and discusses potentially interesting or fruitful strategies for the peptoid biomimetics research community.
View details for DOI 10.1002/bip.21621
View details for Web of Science ID 000295385400003
View details for PubMedID 22180903
A Chemically Synthesized Peptoid-Based Drag-Tag Enhances Free-Solution DNA Sequencing by Capillary Electrophoresis
2011; 96 (5): 702-707
We report a capillary-based DNA sequencing read length of 100 bases in 16 min using end-labeled free-solution conjugate electrophoresis (FSCE) with a monodisperse poly-N-substituted glycine (polypeptoid) as a synthetic drag-tag. FSCE enabled rapid separation of single-stranded (ss) DNA sequencing fragments with single-base resolution without the need for a viscous DNA separation matrix. Protein-based drag-tags previously used for FSCE sequencing, for example, streptavidin, are heterogeneous in molar mass (polydisperse); the resultant band-broadening can make it difficult to obtain the single-base resolution necessary for DNA sequencing. In this study, we synthesized and HPLC-purified a 70mer poly-N-(methoxyethyl)glycine (NMEG) drag-tag with a molar mass of - 11 kDa. The NMEG monomers that comprise this peptoid drag-tag are interesting for bioanalytical applications, because the methoxyethyl side chain's chemical structure is reminiscent of the basic monomer unit of polyethylene glycol, a highly biocompatible commercially available polymer, which, however, is not available in monodisperse preparation at an - 11 kDa molar mass. This is the first report of ssDNA separation and of four-color, base-by-base DNA sequencing by FSCE through the use of a chemically synthesized drag-tag. These results show that high-molar mass, chemically synthesized drag-tags based on the polyNMEG structure, if obtained in monodisperse preparation, would serve as ideal drag-tags and could help FSCE reach the commercially relevant read lengths of 100 bases or more.
View details for DOI 10.1002/bip.21627
View details for Web of Science ID 000295385400018
View details for PubMedID 22180915
NMEGylation: A Novel Modification to Enhance the Bioavailability of Therapeutic Peptides
2011; 96 (5): 688-693
We have evaluated "NMEGylation"--the covalent attachment of an oligo-N-methoxyethylglycine (NMEG) chain--as a new form of peptide/protein modification to enhance the bioavailability of short peptides. OligoNMEGs are hydrophilic polyethylene glycol-like molecules made by solid-phase synthesis, typically up to 40 monomers in length. They have been studied as nonfouling surface coatings and as monodisperse mobility modifiers for free-solution conjugate capillary electrophoresis. However, polyNMEGs have not been demonstrated before this work as modifiers of therapeutic proteins. In prior published work, we identified a short peptide, "C20," as a potential extracellular inhibitor of the fusion of human respiratory syncytial virus with mammalian cells. The present study was aimed at improving the C20 peptide's stability and solubility. To this end, we synthesized and studied a series of NMEGylated C20 peptide-peptoid bioconjugates comprising different numbers of NMEGs at either the N- or C-terminus of C20. NMEGylation was found to greatly improve this peptide's solubility and serum stability; however, longer polyNMEGs (n > 3) deleteriously affected peptide binding to the target protein. By incorporating just one NMEG monomer, along with a glycine monomer as a flexible spacer, at C20's N-terminus (NMEG-Gly-C20), we increased both solubility and serum stability greatly, while recovering a binding affinity comparable to that of unmodified C20 peptide. Our results suggest that NMEGylation with an optimized number of NMEG monomers and a proper linker could be useful, more broadly, as a novel modification to enhance bioavailability and efficacy of therapeutic peptides.
View details for DOI 10.1002/bip.21607
View details for Web of Science ID 000295385400016
View details for PubMedID 22180913
View details for PubMedCentralID PMC3243944
Sustained prolonged topical delivery of bioactive human insulin for potential treatment of cutaneous wounds
INTERNATIONAL JOURNAL OF PHARMACEUTICS
2010; 398 (1-2): 146-154
Skin damaged by heat, radiation, or chemical exposure is difficult to treat and slow to heal. Indeed full restoration of the tissue is difficult to obtain. Sub-dermal insulin injection was recently shown to stimulate wound healing of the skin by accelerating wound closure, stimulating angiogenesis and inducing a regenerative process of healing. We have developed a topical delivery vehicle that is capable of releasing therapeutic levels of bioactive insulin for several weeks with the potential to stimulate and sustain healing. By encapsulating the crystalline form of insulin within poly(d,l-lactide-co-glycolide) microspheres, we succeeded in stabilizing and then releasing bioactive insulin for up to 25 days. To measure bioactivity we used Rat L6 myofibroblasts, stimulated them with this slow release insulin and determined activation of the receptors on the cell surface by quantifying AKT phosphorylation. There was only a minor and gradual decrease in AKT phosphorylation over time. To determine whether the slow release insulin could stimulate keratinocyte migration, wounding was simulated by scratching confluent cultures of human keratinocytes (HaCaT). Coverage of the scratch "wounds" was significantly faster in the presence of insulin released from microspheres than in the insulin-free control. Extended and sustained topical delivery of active insulin from a stable protein crystal-based reservoir shows promise in promoting tissue healing.
View details for DOI 10.1016/j.ijpharm.2010.07.052
View details for Web of Science ID 000282920200019
View details for PubMedID 20691251
Modular enzymatically crosslinked protein polymer hydrogels for in situ gelation
2010; 31 (28): 7288-7297
Biomaterials that mimic the extracellular matrix in both modularity and crosslinking chemistry have the potential to recapitulate the instructive signals that ultimately control cell fate. Toward this goal, modular protein polymer-based hydrogels were created through genetic engineering and enzymatic crosslinking. Animal derived tissue transglutaminase (tTG) and recombinant human transglutaminase (hTG) enzymes were used for coupling two classes of protein polymers containing either lysine or glutamine, which have the recognition substrates for enzymatic crosslinking evenly spaced along the protein backbone. Utilizing tTG under physiological conditions, complete crosslinking occurred within 2 min, as determined by particle tracking microrheology. Hydrogel composition impacted the elastic storage modulus of the gel over 4-fold and also influenced microstructure and degree of swelling, but did not appreciably effect degradation by plasmin. Mouse 3T3 and primary human fibroblasts were cultured in both 2- and 3-dimensions without a decrease in cell viability and displayed spreading in 2D. The properties, which are controlled through the specific nature of the protein polymer precursors, render these gels valuable for in situ therapies. Furthermore, the modular hydrogel composition allows tailoring of mechanical and physical properties for specific tissue engineering applications.
View details for DOI 10.1016/j.biomaterials.2010.06.003
View details for Web of Science ID 000281183000009
View details for PubMedID 20609472
Mimicking SP-C palmitoylation on a peptoid-based SP-B analogue markedly improves surface activity
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
2010; 1798 (9): 1663-1678
Hydrophobic lung surfactant proteins B and C (SP-B and SP-C) are critical for normal respiration in vertebrates, and each comprises specific structural attributes that enable the surface-tension-reducing ability of the lipid-protein mixture in lung surfactant. The difficulty in obtaining pure SP-B and SP-C on a large scale has hindered efforts to develop a non-animal-derived surfactant replacement therapy for respiratory distress. Although peptide-based SP-C mimics exhibit similar activity to the natural protein, helical peptide-based mimics of SP-B benefit from dimeric structures. To determine if in vitro surface activity improvements in a mixed lipid film could be garnered without creating a dimerized structural motif, a helical and cationic peptoid-based SP-B mimic was modified by SP-C-like N-terminus alkylation with octadecylamine. "Hybridized" mono- and dialkylated peptoids significantly decreased the maximum surface tension of the lipid film during cycling on the pulsating bubble surfactometer relative to the unalkylated variant. Peptoids were localized in the fluid phase of giant unilamellar vesicle lipid bilayers, as has been described for SP-B and SP-C. Using Langmuir-Wilhelmy surface balance epifluorescence imaging (FM) and atomic force microscopy (AFM), only lipid-alkylated peptoid films revealed micro- and nanostructures closely resembling films containing SP-B. AFM images of lipid-alkylated peptoid films showed gel condensed-phase domains surrounded by a distinct phase containing "nanosilo" structures believed to enhance re-spreading of submonolayer material. N-terminus alkylation may be a simple, effective method for increasing lipid affinity and surface activity of single-helix SP-B mimics.
View details for DOI 10.1016/j.bbamem.2010.04.012
View details for Web of Science ID 000280752100004
View details for PubMedID 20441770
Biophysical Mimicry of Lung Surfactant Protein B by Random Nylon-3 Copolymers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2010; 132 (23): 7957-7967
Non-natural oligomers have recently shown promise as functional analogues of lung surfactant proteins B and C (SP-B and SP-C), two helical and amphiphilic proteins that are critical for normal respiration. The generation of non-natural mimics of SP-B and SP-C has previously been restricted to step-by-step, sequence-specific synthesis, which results in discrete oligomers that are intended to manifest specific structural attributes. Here we present an alternative approach to SP-B mimicry that is based on sequence-random copolymers containing cationic and lipophilic subunits. These materials, members of the nylon-3 family, are prepared by ring-opening polymerization of beta-lactams. The best of the nylon-3 polymers display promising in vitro surfactant activities in a mixed lipid film. Pulsating bubble surfactometry data indicate that films containing the most surface-active polymers attain adsorptive and dynamic-cycling properties that surpass those of discrete peptides intended to mimic SP-B. Attachment of an N-terminal octadecanoyl unit to the nylon-3 copolymers, inspired by the post-translational modifications found in SP-C, affords further improvements by reducing the percent surface area compression to reach low minimum surface tension. Cytotoxic effects of the copolymers are diminished relative to that of an SP-B-derived peptide and a peptoid-based mimic. The current study provides evidence that sequence-random copolymers can mimic the in vitro surface-active behavior of lung surfactant proteins in a mixed lipid film. These findings raise the possibility that random copolymers might be useful for developing a lung surfactant replacement, which is an attractive prospect given that such polymers are easier to prepare than are sequence-specific oligomers.
View details for DOI 10.1021/ja909734n
View details for Web of Science ID 000278717700042
View details for PubMedID 20481635
Multivalent Protein Polymer MRI Contrast Agents: Controlling Relaxivity via Modulation of Amino Acid Sequence
2010; 11 (6): 1429-1436
Magnetic resonance imaging is a noninvasive imaging modality with high spatial and temporal resolution. Contrast agents (CAs) are frequently used to increase the contrast between tissues of interest. To increase the effectiveness of MR agents, small molecule CAs have been attached to macromolecules. We have created a family of biodegradable, macromolecular CAs based on protein polymers, allowing control over the CA properties. The protein polymers are monodisperse, random coil, and contain evenly spaced lysines that serve as reactive sites for Gd(III) chelates. The exact sequence and length of the protein can be specified, enabling controlled variation in lysine spacing and molecular weight. Relaxivity could be modulated by changing protein polymer length and lysine spacing. Relaxivities of up to approximately 14 mM(-1) s(-1) per Gd(III) and approximately 461 mM(-1) s(-1) per conjugate were observed. These CAs are biodegradable by incubation with plasmin, such that they can be easily excreted after use. They do not reduce cell viability, a prerequisite for future in vivo studies. The protein polymer CAs can be customized for different clinical diagnostic applications, including biomaterial tracking, as a balanced agent with high relaxivity and appropriate molar mass.
View details for DOI 10.1021/bm901378a
View details for Web of Science ID 000278613200002
View details for PubMedID 20420441
Novel Peptoid Building Blocks: Synthesis of Functionalized Aromatic Helix-Inducing Submonomers
2010; 12 (3): 492-495
Peptoids, oligo-N-substituted glycines, can fold into well-defined helical secondary structures. The design and synthesis of new peptoid building blocks that are capable of both (a) inducing a helical secondary structure and (b) decorating the helices with chemical functionalities are reported. Peptoid heptamers containing carboxamide, carboxylic acid or thiol functionalities were synthesized, and the resulting peptoids were shown to form stable helices. A thiol-containing peptoid readily formed the homodisulfide, providing a convenient route to prepare peptoid helix homodimers.
View details for DOI 10.1021/ol902660p
View details for Web of Science ID 000273982600024
View details for PubMedID 20055478
View details for PubMedCentralID PMC2814525
Comparing bacterial membrane interactions of antimicrobial peptides and their mimics.
Methods in molecular biology (Clifton, N.J.)
2010; 618: 171-182
Interactions with bacterial membranes are integral to the mechanisms of action of all antimicrobial peptides (AMPs), regardless of their final cellular targets. Here, we describe in detail two biophysical techniques that can be used to measure the membrane activities of AMPs and antimicrobial peptidomimetics: (1) a calcein leakage assay to investigate interactions between AMPs/peptidomimetics with large unilamellar vesicles and (2) a potential-sensitive dye-based depolarization assay to investigate interactions with the membranes of live bacteria. By comparing the membrane interactions of AMPs and their mimics, these techniques can provide insights into their extent of mimicry and their antimicrobial mechanisms.
View details for DOI 10.1007/978-1-60761-594-1_12
View details for PubMedID 20094865
Chemoselective and Microwave-Assisted Synthesis of Glycopeptoids
2009; 11 (22): 5210-5213
The chemoselective glycosylation of N-alkylaminooxy side chains with unprotected reducing sugars has proven useful for the synthesis of glycopeptides. Herein, we extend the N-alkylaminooxy strategy to the synthesis of glycopeptoids. A N-methylaminooxy submonomer was efficiently synthesized and incorporated into peptoids. Glycosylation of the peptoids proceeded chemoselectively and site-specifically at the N-methylaminooxy moieties. Employing microwave irradiation significantly increased the degree of glycosylation and shortened the reaction times.
View details for DOI 10.1021/ol9021468
View details for Web of Science ID 000271583000030
View details for PubMedID 19905028
Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (46): 19375-19380
The opportunistic pathogen Candida albicans can undergo phenotypic switching between a benign, unicellular phenotype and an invasive, multicellular form that causes candidiasis. Increasingly, strains of Candida are becoming resistant to antifungal drugs, making the treatment of candidiasis difficult, especially in immunocompromised or critically ill patients. Consequently, there is a pressing need to develop new drugs that circumvent fungal drug-resistance mechanisms. In this work we used soft X-ray tomography to image the subcellular changes that occur as a consequence of both phenotypic switching and of treating C. albicans with antifungal peptoids, a class of candidate therapeutics unaffected by drug resistance mechanisms. Peptoid treatment suppressed formation of the pathogenic hyphal phenotype and resulted in striking changes in cell and organelle morphology, most dramatically in the nucleus and nucleolus, and in the number, size, and location of lipidic bodies. In particular, peptoid treatment was seen to cause the inclusion of lipidic bodies into the nucleus.
View details for DOI 10.1073/pnas.0906145106
View details for Web of Science ID 000271907400029
View details for PubMedID 19880740
Engineering Surfaces for Substrate-Mediated Gene Delivery Using Recombinant Proteins
2009; 10 (10): 2779-2786
Immobilized fibronectin and other natural proteins have been utilized to enhance substrate-mediated gene delivery, with apparent contributions from the intrinsic bioactivity and also physical properties of the immobilized proteins. In this report, we investigated the use of recombinant proteins, compared to the full-length fibronectin protein, as surface coatings for gene delivery to investigate the mechanisms by which fibronectin enhances gene transfer. The recombinant fibronectin fragment FNIII(7-10) (FNIII) contains the alpha(5)beta(1) binding domain of fibronectin and supports cell adhesion, whereas the recombinant protein polymer PP-12 is also negatively charged and has a molecular weight similar to FNIII, but lacks cell binding domains. Transfection was compared on surfaces modified with FNIII, full-length fibronectin, or PP-12. The full-length fibronectin provided the greatest extent of transgene expression relative to FNIII or PP-12, which was consistent with the amount of DNA that associated with cells. FNIII had 4.2-fold or 4.7-fold lower expression levels relative to fibronectin for polyplexes and lipoplexes, respectively. PP-12 produced expression levels that were 317-fold and 12.0-fold less than fibronectin for polyplexes and lipoplexes, respectively. Although expression was greater on FNIII relative to PP-12, the levels of DNA associated per cell with FNIII were similar to or less than those with PP-12, suggesting that the bioactive sequences may contribute to an enhanced intracellular trafficking. For lipoplexes delivered on FNIII, the efficiency of intracellular trafficking and levels of caveolar DNA were greater than that observed with either the full-length fibronectin or PP-12. For polyplexes, fibronectin fragment resulted in greater intracellular trafficking efficiency compared to PP-12 protein polymer. Recombinant proteins can be employed in place of full-length extracellular matrix proteins for substrate-mediated gene delivery, and bioactive sequences can influence one or more steps in the gene delivery process to maximize transfection.
View details for DOI 10.1021/bm900628e
View details for Web of Science ID 000270548700009
View details for PubMedID 19775146
Size-based protein separations by microchip electrophoresis using an acid-labile surfactant as a replacement for SDS
2009; 30 (12): 2117-2122
We demonstrate the use of an acid-labile surfactant (ALS) as a replacement for SDS for size-based protein separations in a microfluidic device. ALS is of interest to the proteomic field as it degrades at low pH and hence can be removed to reduce surfactant interference with down-stream MS. A range of SDS and ALS concentrations were tested as denaturants for microchip electrophoresis to investigate their effects on the separation of proteins from 18 to 116 kDa and to provide a suitable comparison between the two surfactants. The electrophoretic mobilities of the proteins were not significantly affected by the use of ALS instead of SDS. Protein separations with ALS are performed in less than 3 min, which is a significant decrease in the time compared with the previous ALS separations on a slab gel format. We also demonstrate the use of poly-N-hydroxyethylacrylamide as a dynamic, hydrophilic chip channel coating that can be applied with a rapid and simple protocol for size-based protein separation. The results reported here could significantly decrease the time and increase the attainable level of automation and integration of the front-end protein fractionation required for "top-down" proteomics.
View details for DOI 10.1002/elps.200800771
View details for Web of Science ID 000268270400010
View details for PubMedID 19582712
DNA migration mechanism analyses for applications in capillary and microchip electrophoresis
2009; 30 (12): 2014-2024
In 2009, electrophoretically driven DNA separations in slab gels and capillaries have the sepia tones of an old-fashioned technology in the eyes of many, even while they remain ubiquitously used, fill a unique niche, and arguably have yet to reach their full potential. For comic relief, what is old becomes new again: agarose slab gel separations are used to prepare DNA samples for "next-gen" sequencing platforms (e.g. the Illumina and 454 machines) - dsDNA molecules within a certain size range are "cut out" of a gel and recovered for subsequent "massively parallel" pyrosequencing. In this review, we give a Barron lab perspective on how our comprehension of DNA migration mechanisms in electrophoresis has evolved, since the first reports of DNA separations by CE ( approximately 1989) until now, 20 years later. Fused-silica capillaries and borosilicate glass and plastic microchips quietly offer increasing capacities for fast (and even "ultra-fast"), efficient DNA separations. While the channel-by-channel scaling of both old and new electrophoresis platforms provides key flexibility, it requires each unique DNA sample to be prepared in its own micro or nanovolume. This Achilles' heel of electrophoresis technologies left an opening through which pooled sample, next-gen DNA sequencing technologies rushed. We shall see, over time, whether sharpening understanding of transitions in DNA migration modes in crosslinked gels, nanogel solutions, and uncrosslinked polymer solutions will allow electrophoretic DNA analysis technologies to flower again. Microchannel electrophoresis, after a quiet period of metamorphosis, may emerge sleeker and more powerful, to claim its own important niche applications.
View details for DOI 10.1002/elps.200900264
View details for Web of Science ID 000268270400002
View details for PubMedID 19582705
Experimental and theoretical investigation of chain length and surface coverage on fouling of surface grafted polypeptoids
2009; 4 (2): FA22-FA32
Numerous strategies exist to prevent biological fouling of surfaces in physiological environments; our strategy focuses on the modification of surfaces with poly-N-substituted glycine oligomers (polypeptoids). We previously reported the synthesis and characterization of three novel polypeptoid polymers that can be used to modify titanium oxide surfaces, rendering the surfaces resistant to adsorption of proteins, to adhesion of mammalian and bacterial cells and to degradation by common protease enzymes. In this study, we investigated the effect of polypeptoid chain length on the antifouling properties of the modified surfaces. For these experiments we used poly(N-methoxyethyl) glycines with lengths between ten and fifty repeat units and determined the influence of chain length on coating thickness and density as well as resistance to protein adsorption and cellular adhesion. Short-term protein resistance remained low for all polymers, as measured by optical waveguide lightmode spectroscopy, while fibroblast adhesion after several weeks indicated reduced fouling resistance for the polypeptoid-modified surfaces with the shortest chain length polymer. Experimental observations were compared to predictions obtained from a molecular theory of polymer and protein adsorption. Good agreement was found between experiment and theory for the chain length dependence of peptoid grafting density, and for protein adsorption as a function of peptoid grafting density. The theoretical predictions provide specific guidelines for the surface coverage for each molecular weight for optimal antifouling. The predictions show the relationship between polymer layer structure and fouling.
View details for DOI 10.1116/1.3115103
View details for Web of Science ID 000266976300004
View details for PubMedID 20300542
Synthesis and Characterization of a New Class of Cationic Protein Polymers for Multivalent Display and Biomaterial Applications
2009; 10 (5): 1125-1134
Monodisperse protein polymers engineered by biosynthetic techniques are well suited to serve as a basis for creating comb-like polymer architectures for biomaterial applications. We have developed a new class of linear, cationic, random-coil protein polymers designed to act as scaffolds for multivalent display. These polymers contain evenly spaced lysine residues that allow for chemical or enzymatic conjugation of pendant functional groups. Circular dichroism spectroscopy and turbidity experiments have confirmed that these proteins have a random coil structure and are soluble up to at least 65 degrees C. Cell viability assays suggest these constructs are nontoxic in solution up to a concentration of 100 microM. We have successfully attached a small bioactive peptide, a peptoid-peptide hybrid, a poly(ethylene glycol) polymer, and a fluorophore to the protein polymers by chemical or enzymatic coupling, demonstrating their suitability to serve as multivalent scaffolds in solutions or as gels.
View details for DOI 10.1021/bm801348g
View details for Web of Science ID 000265914200014
View details for PubMedID 19361214
Self-assembling peptide-lipoplexes for substrate-mediated gene delivery
2009; 5 (3): 903-912
The efficiency of biomaterial-based gene delivery is determined by the interaction of the material and the vector. For lipoplexes, surface immobilization has been used to transfect cells for applications such as cell arrays and model tissue formation through patterned transfection. Further increases in the delivery efficiency are limited by cellular internalization, which may be overcome by altering the material/vector interactions. In this report, we investigated the modification of the lipoplex physical properties through self-assembly with cationic peptides, and subsequently quantified cellular association, internalization and nuclear accumulation of DNA and transfection. Relative to lipid alone, peptide-lipoplexes enhanced transfection by up to 4.6-fold. The presence of the peptide in the lipoplex increased internalization efficiency by up to 4.5-fold, decreased the percentage of lysosomal DNA by 2.1-fold and increased the efficiency of nuclear accumulation by 3.0-fold. In addition, an analysis of internalization pathways for peptide-lipoplexes indicated a greater role of clathrin and caveolae-mediated endocytosis relative to macropinocytosis, which was not observed for peptide-free lipoplexes. These results demonstrate peptide-induced enhancement of gene transfer by surface immobilization due to increased cellular internalization and nuclear accumulation, which has numerous applications ranging from cell-based assays to regenerative medicine.
View details for DOI 10.1016/j.actbio.2008.10.003
View details for Web of Science ID 000264622100011
View details for PubMedID 18990615
Close Mimicry of Lung Surfactant Protein B by "Clicked" Dimers of Helical, Cationic Peptoids
2009; 92 (6): 538-553
A family of peptoid dimers developed to mimic SP-B is presented, where two amphipathic, cationic helices are linked by an achiral octameric chain. SP-B is a vital therapeutic protein in lung surfactant replacement therapy, but its large-scale isolation or chemical synthesis is impractical. Enhanced biomimicry of SP-B's disulfide-bonded structure has been previously attempted via disulfide-mediated dimerization of SP-B(1-25) and other peptide mimics, which improved surface activity relative to the monomers. Herein, the effects of disulfide- or "click"-mediated (1,3-dipolar cycloaddition) dimerization, as well as linker chemistry, on the lipid-associated surfactant activity of a peptoid monomer are described. Results revealed that the 'clicked' peptoid dimer enhanced in vitro surface activity in a DPPC:POPG:PA lipid film relative to its disulfide-bonded and monomeric counterparts in both surface balance and pulsating bubble surfactometry studies. On the pulsating bubble surfactometer, the film containing the "clicked" peptoid dimer outperformed all presented peptoid monomers and dimers, and two SP-B derived peptides, attaining an adsorbed surface tension of 22 mN m(-1), and maximum and minimum cycling values of 42 mN m(-1) and near-zero, respectively.
View details for DOI 10.1002/bip.21309
View details for Web of Science ID 000272364900008
View details for PubMedID 19777571
View details for PubMedCentralID PMC2860423
Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods
2008; 29 (23): 4618-4626
The reference human genome provides an adequate basis for biological researchers to study the relationship between genotype and the associated phenotypes, but a large push is underway to sequence many more genomes to determine the role of various specificities among different individuals that control these relationships and to enable the use of human genome data for personalized and preventative healthcare. The current electrophoretic methodology for sequencing an entire mammalian genome, which includes standard molecular biology techniques for genomic sample preparation and the separation of DNA fragments using capillary array electrophoresis, remains far too expensive ($5 million) to make genome sequencing ubiquitous. The National Human Genome Research Institute has put forth goals to reduce the cost of human genome sequencing to $100,000 in the short term and $1000 in the long term to spur the innovative development of technologies that will permit the routine sequencing of human genomes for use as a diagnostic tool for disease. Since the announcement of these goals, several companies have developed and released new, non-electrophoresis-based sequencing instruments that enable massive throughput in the gathering of genomic information. In this review, we discuss the advantages and limitations of these new, massively parallel sequencers and compare them with the currently developing next generation of electrophoresis-based genetic analysis platforms, specifically microchip electrophoresis devices, in the context of three distinct types of genetic analysis.
View details for DOI 10.1002/elps.200800456
View details for Web of Science ID 000261931200002
View details for PubMedID 19053153
DNA sequencing by microchip electrophoresis using mixtures of high- and low-molar mass poly(N,N-dimethylacrylamide) matrices
2008; 29 (23): 4663-4668
Previous studies have reported that mixed molar mass polymer matrices show enhanced DNA sequencing fragment separation compared with matrices formulated from a single average molar mass. Here, we describe a systematic study to investigate the effects of varying the amounts of two different average molar mass polymers on the DNA sequencing ability of poly(N,N-dimethylacrylamide) (pDMA) sequencing matrices in microfluidic chips. Two polydisperse samples of pDMA, with weight-average molar masses of 3.5 MDa and 770 kDa, were mixed at various fractional concentrations while maintaining the overall polymer concentration at 5% w/v. We show that although the separation of short DNA fragments depends strongly on the overall solution concentration of the polymer, inclusion of the high-molar mass polymer is essential to achieve read lengths of interest (>400 bases) for many sequencing applications. Our results also show that one of the blended matrices, comprised of 3% 3.5 MDa pDMA and 2% 770 kDa pDMA, yields similar sequencing read lengths (>520 bases on average) to the high-molar mass matrix alone, while also providing a fivefold reduction in zero-shear viscosity. These results indicate that the long read lengths achieved in a viscous, high-molar mass polymer matrix are also possible to achieve in a tuned, blended matrix of high- and low-molar mass polymers with a much lower overall solution viscosity.
View details for DOI 10.1002/elps.200800389
View details for Web of Science ID 000261931200007
View details for PubMedID 19053157
Hydrophobically modified polyacrylamide block copolymers for fast, high-resolution DNA sequencing in microfluidic chips
2008; 29 (23): 4669-4676
By using a microfluidic electrophoresis platform to perform DNA sequencing, genomic information can be obtained more quickly and affordably than the currently employed capillary array electrophoresis instruments. Previous research in our group has shown that physically cross-linked, hydrophobically modified polyacrylamide matrices separate dsDNA more effectively than linear polyacrylamide (LPA) solutions. Expanding upon this work, we have synthesized a series of LPA-co-dihexylacrylamide block copolymers specifically designed to electrophoretically sequence ssDNA quickly and efficiently on a microfluidic device. By incorporating very small amounts of N,N-dihexylacrylamide, a hydrophobic monomer, these copolymer solutions achieved up to approximately 10% increases in average DNA sequencing read length over LPA homopolymer solutions of matched molar mass. Additionally, the inclusion of the small amount of hydrophobe does not significantly increase the polymer solution viscosities, relative to LPA solutions, so that channel loading times between the copolymers and the homopolymers are similar. The resulting polymer solutions are capable of providing enhanced sequencing separations in a short period of time without compromising the ability to rapidly load and unload the matrix from a microfluidic device.
View details for DOI 10.1002/elps.200800353
View details for Web of Science ID 000261931200008
View details for PubMedID 19053064
Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: A comparison with commercially available materials
2008; 29 (23): 4652-4662
Electrophoresis-based DNA sequencing is the only proven technology for the de novo sequencing of large and complex genomes. Miniaturization of capillary array electrophoresis (CAE) instruments can increase sequencing throughput and decrease cost while maintaining the high quality and long read lengths that has made CAE so successful for de novo sequencing. The limited availability of high-performance polymer matrices and wall coatings designed specifically for microchip-sequencing platforms continues to be a major barrier to the successful development of a commercial microchip-sequencing instrument. It has been generally assumed that the matrices and wall coatings that have been developed for use in commercial CAE instruments will be able to be implemented directly into microchip devices with little to no change in sequencing performance. Here, we show that sequencing matrices developed specifically for microchip electrophoresis systems can deliver read lengths that are 150-300 bases longer on chip than some of the most widely used polymer-sequencing matrices available commercially. Additionally, we show that the coating ability of commercial matrices is much less effective in the borosilicate chips used in this study. These results lead to the conclusion that new materials must be developed to make high-performance microfabricated DNA-sequencing instruments a reality.
View details for DOI 10.1002/elps.200800352
View details for Web of Science ID 000261931200006
View details for PubMedID 19053156
Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device
2008; 29 (23): 4751-4760
We have developed a new method for the analysis of low abundant point mutations in genomic DNA using a combination of an allele-specific ligase detection reaction (LDR) with free-solution conjugate electrophoresis (FSCE) to generate and analyze the genetic products. FSCE eliminates the need for a polymer sieving matrix by conjugating chemically synthesized polyamide "drag-tags" onto the LDR primers. The additional drag of the charge-neutral drag-tag breaks the linear scaling of the charge-to-friction ratio of DNA and enables size-based separations of DNA in free solution using electrophoresis with no sieving matrix. We successfully demonstrate the conjugation of polyamide drag-tags onto a set of four LDR primers designed to probe the K-ras oncogene for mutations highly associated with colorectal cancer, the simultaneous generation of fluorescently labeled LDR/drag-tag conjugate (LDR-dt) products in a multiplexed, single-tube format with mutant:WT ratios as low as 1:100, respectively, and the single-base, high-resolution separation of all four LDR-dt products. Separations were conducted in free solution with no polymer network using both a commercial capillary array electrophoresis (CAE) system and a PMMA microchip replicated via hot-embossing with only a Tris-based running buffer containing additives to suppress the EOF. Typical analysis times for LDR-dt were 11 min using the CAE system and as low as 85 s for the PMMA microchips. With resolution comparable to traditional gel-based CAE, FSCE along with microchip electrophoresis decreased the separation time by more than a factor of 40.
View details for DOI 10.1002/elps.200800197
View details for Web of Science ID 000261931200017
View details for PubMedID 19053073
Thermoresponsive N-alkoxyalkylacrylamide polymers as a sieving matrix for high-resolution DNA separations on a microfluidic chip
2008; 29 (23): 4677-4683
In recent years, there has been an increasing demand for a wide range of DNA separations that require the development of materials to meet the needs of high resolution and high throughput. Here, we demonstrate the use of thermoresponsive N-alkoxyalkylacrylamide polymers as a sieving matrix for DNA separations on a microfluidic chip. The viscosities of the N-alkoxyalkylacrylamide polymers are more than an order of magnitude lower than that of a linear polyacrylamide (LPA) of corresponding molecular weight, allowing rapid loading of the microchip. At 25 degrees C, N-alkoxyalkylacrylamide polymers can provide improved DNA separations compared with LPA in terms of reduced separation time and increased separation efficiency, particularly for the larger DNA fragments. The improved separation efficiency in N-alkoxyalkylacrylamide polymers is attributed to the peak widths increasing only slightly with DNA fragment size, while the peak widths increase appreciably above 150 bp using an LPA matrix. Upon elevating the temperature to 50 degrees C, the increase in viscosity of the N-alkoxyalkylacrylamide solutions is dependent upon their overall degree of hydrophobicity. The most hydrophobic polymers exhibit a lower critical solution temperature below 50 degrees C, undergoing a coil-to-globule transition followed by chain aggregation. DNA separation efficiency at 50 degrees C therefore decreases significantly with increasing hydrophobic character of the polymers, and no separations were possible with solutions with a lower critical solution temperature below 50 degrees C. The work reported here demonstrates the potential for this class of polymers to be used for applications such as PCR product and RFLP sizing, and provides insight into the effect of polymer hydrophobicity on DNA separations.
View details for DOI 10.1002/elps.200800354
View details for Web of Science ID 000261931200009
View details for PubMedID 19053065
Peptide-Mediated Lipofection Is Governed by Lipoplex Physical Properties and the Density of Surface-Displayed Amines
JOURNAL OF PHARMACEUTICAL SCIENCES
2008; 97 (11): 4794-4806
Peptides can potentiate lipid-mediated gene delivery by modifying lipoplex physiochemical properties to overcome rate-limiting steps to gene transfer. The objectives of this study were to determine the regimes over which cationic peptides enhance lipofection and to investigate the mechanism of action, such as increased cellular association resulting from changes in lipoplex physical properties. Short, cationic peptides were incorporated into lipoplexes by mixing peptide, lipid and DNA. Lipoplexes were characterized using gel retardation, dynamic light scattering, and fluorescent microscopy, and the amount of surface-displayed amines was quantified by fluorescamine. Size, zeta potential, and surface amines for lipoplexes were dependent on peptide/DNA ratio. Inclusion of peptides in lipoplexes resulted in up to a 13-fold increase in percentage of cells transfected, and up to a 76-fold increase in protein expression. This transfection enhancement corresponded to a small particle diameter and positive zeta potential of lipoplexes, as well as increased amount of surface-displayed amines. Relative to lipid alone, these properties of the peptide-modified lipoplexes enhanced cellular association, which has been reported as a rate-limiting step for transfection with lipoplexes. The addition of peptides is a simple method of lipofection enhancement, as direct chemical modification of lipids is not necessary for increased transfection.
View details for DOI 10.1002/jps.21338
View details for Web of Science ID 000260607100010
View details for PubMedID 18306277
Biomimicry of Surfactant Protein C
ACCOUNTS OF CHEMICAL RESEARCH
2008; 41 (10): 1409-1417
Since the widespread use of exogenous lung surfactant to treat neonatal respiratory distress syndrome, premature infant survival and respiratory morbidity have dramatically improved. Despite the effectiveness of the animal-derived surfactant preparations, there still remain some concerns and difficulties associated with their use. This has prompted investigation into the creation of synthetic surfactant preparations. However, to date, no clinically used synthetic formulation is as effective as the natural material. This is largely because the previous synthetic formulations lacked analogues of the hydrophobic proteins of the lung surfactant system, SP-B and SP-C, which are critical functional constituents. As a result, recent investigation has turned toward the development of a new generation of synthetic, biomimetic surfactants that contain synthetic phospholipids along with a mimic of the hydrophobic protein portion of lung surfactant. In this Account, we detail our efforts in creating accurate mimics of SP-C for use in a synthetic surfactant replacement therapy. Despite SP-C's seemingly simple structure, the predominantly helical protein is extraordinarily challenging to work with given its extreme hydrophobicity and structural instability, which greatly complicates the creation of an effective SP-C analogue. Drawing inspiration from Nature, two promising biomimetic approaches have led to the creation of rationally designed biopolymers that recapitulate many of SP-C's molecular features. The first approach utilizes detailed SP-C structure-activity relationships and amino acid folding propensities to create a peptide-based analogue, SP-C33. In SP-C33, the problematic and metastable polyvaline helix is replaced with a structurally stable polyleucine helix and includes a well-placed positive charge to prevent aggregation. SP-C33 is structurally stable and eliminates the association propensity of the native protein. The second approach follows the same design considerations but makes use of a non-natural, poly-N-substituted glycine or "peptoid" scaffold to circumvent the difficulties associated with SP-C. By incorporating unique biomimetic side chains in a non-natural backbone, the peptoid mimic captures both SP-C's hydrophobic patterning and its helical secondary structure. Despite the differences in structure, both SP-C33 and the SP-C peptoid mimic capture many requisite features of SP-C. In a surfactant environment, these analogues also replicate many of the key surface activities necessary for a functional biomimetic surfactant therapy while overcoming the difficulties associated with the natural protein. With improved stability, greater production potential, and elimination of possible pathogenic contamination, these biomimetic surfactant formulations offer not only the potential to improve the treatment of respiratory distress syndrome but also the opportunity to treat other respiratory-related disorders.
View details for DOI 10.1021/ar800058t
View details for Web of Science ID 000260254300018
View details for PubMedID 18834153
A forensic laboratory tests the Berkeley microfabricated capillary array electrophoresis device
59th Annual Meeting of the American-Academy-of-Forensic-Science
BLACKWELL PUBLISHING. 2008: 828–37
Miniaturization of capillary electrophoresis onto a microchip for forensic short tandem repeat analysis is the initial step in the process of producing a fully integrated and automated analysis system. A prototype of the Berkeley microfabricated capillary array electrophoresis device was installed at the Virginia Department of Forensic Science for testing. Instrument performance was verified by PowerPlex 16 System profiling of single source, sensitivity series, mixture, and casework samples. Mock sexual assault samples were successfully analyzed using the PowerPlex Y System. Resolution was assessed using the TH01, CSF1PO, TPOX, and Amelogenin loci and demonstrated to be comparable with commercial systems along with the instrument precision. Successful replacement of the Hjerten capillary coating method with a dynamic coating polymer was performed. The accurate and rapid typing of forensic samples demonstrates the successful technology transfer of this device into a practitioner laboratory and its potential for advancing high-throughput forensic typing.
View details for DOI 10.1111/j.1556-4029.2008.00750.x
View details for Web of Science ID 000257664300012
View details for PubMedID 18540973
Sequencing of DNA by free-solution capillary electrophoresis using a genetically engineered protein polymer drag-tag
2008; 80 (8): 2842-2848
We demonstrate the first use of a non-natural, genetically engineered protein polymer drag-tag to sequence DNA fragments by end-labeled free-solution electrophoresis (ELFSE). Fluorescently labeled DNA fragments resulting from the Sanger cycle sequencing reaction were separated by free-solution capillary electrophoresis, with much higher resolution and cleaner results than previously reported for this technique. With ELFSE, size-based separation of DNA in the absence of a sieving matrix is enabled by the end-on attachment of a polymeric "drag-tag" that modifies the charge-to-friction ratio of DNA in a size-dependent fashion. Progress in ELFSE separations has previously been limited by the lack of suitable large, monodisperse drag-tags. To address this problem, we designed, constructed, cloned, expressed, and purified a non-natural, genetically engineered 127mer protein polymer for use as an ELFSE drag-tag. The Sanger cycle sequencing reaction is performed with the drag-tag covalently attached to the sequencing primer, a major advance over previous strategies for ELFSE sequencing. The electrophoretic separation is diffusion-limited, without significant adsorption of the drag-tag to capillary walls. Although the read length (at about 180 bases) is still short, our results provide evidence that larger protein polymer drag-tags, currently under development, could extend the read length of ELFSE to more competitive levels. ELFSE offers the possibility of very rapid DNA sequencing separations without any of the difficulties associated with viscous polymeric sieving networks and hence will be amenable to implementation in microchannel and chip-based electrophoresis systems.
View details for DOI 10.1021/ac702591t
View details for Web of Science ID 000254969100026
View details for PubMedID 18318549
Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2008; 105 (8): 2794-2799
Antimicrobial peptides (AMPs) and their mimics are emerging as promising antibiotic agents. We present a library of "ampetoids" (antimicrobial peptoid oligomers) with helical structures and biomimetic sequences, several members of which have low-micromolar antimicrobial activities, similar to cationic AMPs like pexiganan. Broad-spectrum activity against six clinically relevant BSL2 pathogens is also shown. This comprehensive structure-activity relationship study, including circular dichroism spectroscopy, minimum inhibitory concentration assays, hemolysis and mammalian cell toxicity studies, and specular x-ray reflectivity measurements shows that the in vitro activities of ampetoids are strikingly similar to those of AMPs themselves, suggesting a strong mechanistic analogy. The ampetoids' antibacterial activity, coupled with their low cytotoxicity against mammalian cells, make them a promising class of antimicrobials for biomedical applications. Peptoids are biostable, with a protease-resistant N-substituted glycine backbone, and their sequences are highly tunable, because an extensive diversity of side chains can be incorporated via facile solid-phase synthesis. Our findings add to the growing evidence that nonnatural foldamers will emerge as an important class of therapeutics.
View details for DOI 10.1073/pnas.0708254105
View details for Web of Science ID 000253567900011
View details for PubMedID 18287037
Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C
2008; 47 (6): 1808-1818
The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.
View details for DOI 10.1021/bi7021975
View details for Web of Science ID 000252940600035
View details for PubMedID 18197709
Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2008; 105 (2): 476-481
To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.
View details for DOI 10.1073/pnas.0705093105
View details for Web of Science ID 000252551100017
View details for PubMedID 18184818
Protein, cell and bacterial fouling resistance of polypeptoid-modified surfaces: effect of side-chain chemistry
2008; 4 (1): 131-139
Peptidomimetic polymers consisting of poly-N-substituted glycine oligomers (polypeptoids) conjugated to biomimetic adhesive polypeptides were investigated as antifouling surface coatings. The polymers were immobilized onto TiO(2) surfaces via an anchoring peptide consisting of alternating residues of 3,4-dihydroxyphenylalanine (DOPA) and lysine. Three polypeptoid side-chain compositions were investigated for antifouling performance and stability toward enzymatic degradation. Ellipsometry and XPS analysis confirmed that purified polymers adsorbed strongly to TiO(2) surfaces, and the immobilized polymers were resistant to enzymatic degradation as demonstrated by mass spectrometry. All polypeptoid-modified surfaces exhibited significant reductions in adsorption of lysozyme, fibrinogen and serum proteins, and were resistant to 3T3 fibroblast cell attachment for up to seven days. Long-term in vitro cell attachment studies conducted for six weeks revealed the importance of polypeptoid side-chain composition, with a methoxyethyl side chain providing superior long-term fouling resistance compared to hydroxyethyl and hydroxypropyl side chains. Finally, attachment of both gram-positive and gram-negative bacteria for up to four days under continuous-flow conditions was significantly reduced on the polypeptoid-modified surfaces compared to unmodified TiO(2) surfaces. The results reveal the influence of polypeptoid side-chain chemistry on short-term and long-term protein, cell and bacterial fouling resistance.
View details for DOI 10.1039/b711944e
View details for Web of Science ID 000251580600014
- Protein and peptide biomimicry: Gold-mining inspiration from nature's ingenuity AICHE JOURNAL 2008; 54 (1): 2-8
Surface-immobilised antimicrobial peptoids
2008; 24 (6): 439-448
Surface modification techniques that create surfaces capable of killing adherent bacteria are promising solutions to infections associated with implantable medical devices. Antimicrobial (AM) peptoid oligomers (ampetoids) that were designed to mimic helical AM peptides were synthesised with a peptoid spacer chain to allow mobility and an adhesive peptide moiety for easy and robust immobilisation onto substrata. TiO(2) substrata were modified with the ampetoids and subsequently backfilled with an antifouling (AF) polypeptoid polymer in order to create polymer surface coatings composed of both AM (active) and AF (passive) peptoid functionalities. Confocal microscopy images showed that the membranes of adherent E. coli cells were damaged after 2-h exposure to the modified substrata, suggesting that ampetoids retain AM properties even when immobilised on substrata.
View details for DOI 10.1080/08927010802331829
View details for Web of Science ID 000258594100004
View details for PubMedID 18696290
View details for PubMedCentralID PMC2654338
Use of a genetically engineered protein for the design of a multivalent MR1 contrast agent
2007; 18 (6): 1697-1700
The majority of clinically used contrast agents (CAs) for magnetic resonance imaging have low relaxivities and thus require high concentrations for signal enhancement. Research has turned to multivalent, macromolecular CAs to increase CA efficiency. However, previously developed macromolecular CAs do not provide high relaxivities, have limited biocompatibility, and/or do not have a structure that is readily modifiable to tailor to particular applications. We report a new family of multivalent, biomacromolecular, genetically engineered protein polymer-based CAs; the protein backbone contains evenly spaced lysines that are derivatized with gadolinium (Gd(III)) chelators. The protein's length and repeating amino acid sequence are genetically specified. We reproducibly obtained conjugates with an average of 8-9 Gd(III) chelators per protein. These multivalent CAs reproducibly provide a high relaxivity of 7.3 mM (-1) s (-1) per Gd(III) and 62.6 mM (-1) s (-1) per molecule. Furthermore, they can be incorporated into biomaterial hydrogels via chemical cross-linking of the remaining free lysines, and provide a dramatic contrast enhancement. Thus, these protein polymer CAs could be a useful tool for following the evolution of tissue engineering scaffolds.
View details for DOI 10.1021/bc700149uCCC:$37.00
View details for Web of Science ID 000251166400001
View details for PubMedID 17927227
Stochastic single-molecule Videomicroscopy methods to measure electrophoretic DNA migration modalities in polymer solutions above and below entanglement
2007; 79 (20): 7740-7747
We have studied the effects of polymer molar mass and concentration on the electrophoretic migration modalities of individual molecules of DNA in LPA, HEC, and PEO solutions via epifluorescent videomicroscopy. While both transient entanglement coupling (TEC) and reptation have been studied in the past, the transition between them has not. Understanding this transition will allow for polymer network properties to be optimized to enhance the speed and resolution of DNA separations in microfluidic devices. Near the overlap threshold concentration, C*, TEC is the dominant observed mode of DNA migration, and the observation frequency of TEC increases with increasing polymer molar mass. As polymer concentration is increased, observed TEC events reduce to zero while DNA reptation events become the only detected mechanism. Individual DNA molecules undergoing both migration mechanisms were counted in solutions of varying polymer molar masses and concentrations and were plotted against a dimensionless polymer concentration, C/C*. The data for LPA reduce to form universal curves with a sharp increase in DNA reptation at approximately 6.5C*. Analogous transition concentrations for PEO and HEC were observed at 5C* and 3.5C*, respectively, reflecting the different physical properties of these polymers. This transition correlates closely with the polymer network entanglement concentration, Ce, as measured by rheological techniques. The electrophoretic mobility of lambda-DNA in LPA polymer solutions was also measured and shows how a balance can be struck between DNA resolution and separation speed by choosing the desired prevalence of DNA reptation.
View details for DOI 10.1021/ac071160x
View details for Web of Science ID 000250173200019
View details for PubMedID 17874850
Lipid composition greatly affects the in vitro surface activity of lung surfactant protein mimics
COLLOIDS AND SURFACES B-BIOINTERFACES
2007; 57 (1): 37-55
A crucial aspect of developing a functional, biomimetic lung surfactant (LS) replacement is the selection of the synthetic lipid mixture and surfactant proteins (SPs) or suitable mimics thereof. Studies elucidating the roles of different lipids and surfactant proteins in natural LS have provided critical information necessary for the development of synthetic LS replacements that offer performance comparable to the natural material. In this study, the in vitro surface-active behaviors of peptide- and peptoid-based mimics of the lung surfactant proteins, SP-B and SP-C, were investigated using three different lipid formulations. The lipid mixtures were chosen from among those commonly used for the testing and characterization of SP mimics--(1) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol 7:3 (w/w) (PCPG), (2) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol:palmitic acid 68:22:9 (w/w) (TL), and (3) dipalmitoyl phosphatidylcholine:palmitoyloleoyl phosphatidylcholine:palmitoyloleoyl phosphatidylglycerol:palmitoyloleoyl phosphatidylethanolamine:palmitoyloleoyl phosphatidylserine:cholesterol 16:10:3:1:3:2 (w/w) (IL). The lipid mixtures and lipid/peptide or lipid/peptoid formulations were characterized in vitro using a Langmuir-Wilhelmy surface balance, fluorescent microscopic imaging of surface film morphology, and a pulsating bubble surfactometer. Results show that the three lipid formulations exhibit significantly different surface-active behaviors, both in the presence and absence of SP mimics, with desirable in vitro biomimetic behaviors being greatest for the TL formulation. Specifically, the TL formulation is able to reach low-surface tensions at physiological temperature as determined by dynamic PBS and LWSB studies, and dynamic PBS studies show this to occur with a minimal amount of compression, similar to natural LS.
View details for DOI 10.1016/j.colsurfb.2007.01.001
View details for Web of Science ID 000246750200006
View details for PubMedID 17287113
Electric and hydrodynamic stretching of DNA-polymer conjugates in free-solution electrophoresis
JOURNAL OF CHEMICAL PHYSICS
2007; 126 (17)
The conjugation of an uncharged polymer to DNA fragments makes it possible to separate DNA by free-solution electrophoresis. This end-labeled free-solution electrophoresis method has been shown to successfully separate ssDNA with single monomer resolution up to about 110 bases. It is the aim of this paper to investigate in more detail the coupled hydrodynamic and electrophoretic deformation of the ssDNA-label conjugate at fields below 400 V/cm. Our model is an extension of the theoretical approach originally developed by Stigter and Bustamante [Biophys. J. 75, 1197 (1998)] to investigate the problems of a tethered chain stretching in a hydrodynamic flow and of the electrophoretic stretch of a tethered polyelectrolyte. These two separate models are now used together since the charged DNA is "tethered" to the uncharged polymer (and vice versa), and the resulting self-consistent model is used to predict the deformation and the electrophoretic velocity for the hybrid molecule. Our theoretical and experimental results are in good qualitative agreement.
View details for DOI 10.1063/1.2730799
View details for Web of Science ID 000246284800041
View details for PubMedID 17492889
Multiplexed p53 mutation detection by free-solution conjugate microchannel electrophoresis with polyamide drag-tags
2007; 79 (5): 1848-1854
We report a new, bioconjugate approach to performing highly multiplexed single-base extension (SBE) assays, which we demonstrate by genotyping a large panel of point mutants in exons 5-9 of the p53 gene. A series of monodisperse polyamide "drag-tags" was created using both chemical and biological synthesis and used to achieve the high-resolution separation of genotyping reaction products by microchannel electrophoresis without a polymeric sieving matrix. A highly multiplexed SBE reaction was performed in which 16 unique drag-tagged primers simultaneously probe 16 p53 gene loci, with an abbreviated thermal cycling protocol of only 9 min. The drag-tagged SBE products were rapidly separated by free-solution conjugate electrophoresis (FSCE) in both capillaries and microfluidic chips with genotyping accuracy in excess of 96%. The separation requires less than 70 s in a glass microfluidic chip, or about 20 min in a commercial capillary array sequencing instrument. Compared to gel electrophoresis, FSCE offers greater freedom in the design of SBE primers by essentially decoupling the length of the primer and the electrophoretic mobility of the genotyping products. FSCE also presents new possibilities for the facile implementation of SBE on integrated microfluidic electrophoresis devices for rapid, high-throughput genetic mutation detection or SNP scoring.
View details for DOI 10.1021/ac061903z
View details for Web of Science ID 000244497300008
View details for PubMedID 17256875
Effects of including an N-terminal insertion region and arginine-mimetic side chains in helical peptoid analogues of lung surfactant protein B
2006; 45 (39): 11809-11818
Surfactant protein B (SP-B) is one of two helical, amphipathic proteins critical for the biophysical functioning of lung surfactant (LS) and hence is an important therapeutic protein. This small, complex 79mer has three internal disulfide bonds and homodimerizes via another disulfide bridge. A helical, amphipathic 25mer from the amino terminus (SP-B(1-25)) exhibits surface-active properties similar to those of full-length, synthetic SP-B. In previous work, we created helical, non-natural mimics of SP-B(1-25) based on sequence-specific peptoid 17mers and demonstrated their biomimetic surface activity. Like SP-B(1-25), the peptoids were designed to adopt helical structures with cationic and nonpolar faces. Here, we compare the surface activities of six different helical peptoid analogues of SP-B(1-25) to investigate the importance of mimicking its N-terminal insertion domain as well as its two arginine residues, both thought to be important for the peptide's proper function. Although the peptoid analogues of SP-B(1-25) studied here share many similar features and all functionally mimic SP-B(1-25) to some degree, it is notable that small differences in their sequences and side chain chemistries lead to substantial differences in their observed interactions with a lipid film. A peptoid comprising a hydrophobic, helical insertion region with aromatic side chains shows more biomimetic surface activity than simpler peptoids, and even better activity, by comparison to natural LS, than SP-B(1-25). However, the substitution of lysine-like side chains for arginine-like side chains in the peptoid has little effect on biomimetic surface activity, indicating that interactions of the guanidino groups with lipids may not be critical for the function of these SP-B mimics.
View details for DOI 10.1021/bi060617e
View details for Web of Science ID 000240752400010
View details for PubMedID 17002281
An optimized microchip electrophoresis system for mutation detection by tandem SSCP and heteroduplex analysis for p53 gene exons 5-9
2006; 27 (19): 3823-3835
With the complete sequencing of the human genome, there is a growing need for rapid, highly sensitive genetic mutation detection methods suitable for clinical implementation. DNA-based diagnostics such as single-strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are commonly used in research laboratories to screen for mutations, but the slab gel electrophoresis (SGE) format is ill-suited for routine clinical use. The translation of these assays from SGE to microfluidic chips offers significant speed, cost, and sensitivity advantages; however, numerous parameters must be optimized to provide highly sensitive mutation detection. Here we present a methodical study of system parameters including polymer matrix, wall coating, analysis temperature, and electric field strengths on the effectiveness of mutation detection by tandem SSCP/HA for DNA samples from exons 5-9 of the p53 gene. The effects of polymer matrix concentration and average molar mass were studied for linear polyacrylamide (LPA) solutions. We determined that a matrix of 8% w/v 600 kDa LPA provides the most reliable SSCP/HA mutation detection on chips. The inclusion of a small amount of the dynamic wall-coating polymer poly-N-hydroxyethylacrylamide in the matrix substantially improves the resolution of SSCP conformers and extends the coating lifetime. We investigated electrophoresis temperatures between 17 and 35 degrees C and found that the lowest temperature accessible on our chip electrophoresis system gives the best condition for high sensitivity of the tandem SSCP/HA method, especially for the SSCP conformers. Finally, the use of electrical fields between 350 and 450 V/cm provided rapid separations (<10 min) with well-resolved DNA peaks for both SSCP and HA.
View details for DOI 10.1002/elps.200600358
View details for Web of Science ID 000241621000016
View details for PubMedID 16972304
What is the future of electrophoresis in large-scale genomic sequencing?
2006; 27 (19): 3689-3702
Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.
View details for DOI 10.1002/elps.200600408
View details for Web of Science ID 000241621000002
View details for PubMedID 17031784
The potential of electrophoretic mobility shift assays for clinical mutation detection
2006; 27 (19): 3805-3815
As the understanding of the links between genetic mutations and diseases continues to grow, there is an increasing need for techniques that can rapidly, inexpensively, and sensitively detect DNA sequence alterations. Typically, such analyses are performed on PCR-amplified gene regions. Automated DNA sequencing by capillary array electrophoresis can be used, but is expensive to apply to large numbers of patient samples and/or large genes, and may not always reveal low-abundance mutations in heterozygous samples. Many different types of genetic differences need to be detected, including single-base substitutions and larger sequence alterations such as insertions, deletions, and inversions. Electrophoretic mobility shift assays seem well suited to this purpose and could be used for the efficient screening of patient samples for sequence alterations, effectively reducing the number of samples that must be subjected to full and careful sequencing. While there is much promise, many of the mobility shift assays presently under development have yet to be demonstrated to have the high sensitivity and specificity of mutation detection required for routine clinical application. Hence, further studies and optimization are required, in particular the application of these methods not only to particular genes but also to large numbers of patient samples in blinded studies aimed at the rigorous determination of sensitivity and specificity. This review examines the state-of-the-art of the most commonly used mobility shift assays for mutation detection, including denaturing gradient gel electrophoresis, TGGE, SSCP, heteroduplex analysis, and denaturing HPLC.
View details for DOI 10.1002/elps.200600421
View details for Web of Science ID 000241621000014
View details for PubMedID 17031787
A bio-barcode assay for on-chip attomolar-sensitivity protein detection
LAB ON A CHIP
2006; 6 (10): 1293-1299
Functionalized nanoparticles hold great promise in realizing highly sensitive and selective biodetection. We report a single disposable chip which is capable of carrying out a multi-step process that employs nanoparticles--a bio-barcode assay (BCA) for single protein marker detection. To illustrate the capability of the system, we tested for the presence of prostate specific antigen (PSA) in buffer solution and goat serum. Detection was accomplished at PSA concentrations as low as 500 aM. This corresponds to only 300 copies of protein analytes using 1 microL total sample volume. We established that the on-chip BCA for PSA detection offers four orders of magnitude higher sensitivity compared to commercially available ELISA-based PSA tests.
View details for DOI 10.1039/b606294f
View details for Web of Science ID 000241731200012
View details for PubMedID 17102842
Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics
2006; 78 (13): 4409-4415
We describe a novel class of DNA separation media for microchip electrophoresis, "physically cross-linked" block copolymer networks, which provide rapid (<4.5 min) and remarkably enhanced resolution of DNA in a size range critical for genotyping. Linear poly(acrylamide-co-dihexylacrylamide) (LPA-co-DHA) comprising as little as 0.13 mol % dihexylacrylamide yields substantially improved electrophoretic DNA separations compared to matched molar mass linear polyacrylamide. Single-molecule videomicroscopic images of DNA electrophoresis reveal novel chain dynamics in LPA-co-DHA matrixes, resembling inchworm movement, to which we attribute the increased DNA resolution. Substantial improvements in DNA peak separation are obtained, in particular, in LPA-co-DHA solutions at polymer/copolymer concentrations near the interchain entanglement threshold. Higher polymer concentrations yield enhanced separations only for small DNA molecules (<120 base pairs). Hydrophobically cross-linked networks offer advantages over conventional linear polymers based on enhanced separation performance (or speed) and over chemically cross-linked gels because hydrophobic cross-links can be reversibly broken, allowing facile microchannel loading.
View details for DOI 10.1021/ac060193u
View details for Web of Science ID 000238665200026
View details for PubMedID 16808448
Free-solution electrophoresis of DNA modified with drag-tags at both ends
2006; 27 (9): 1702-1712
In end-labeled free-solution electrophoresis (ELFSE), DNA molecules are labeled with a frictional modifier or "drag-tag", allowing their size-based electrophoretic separation in free solution. Among the interesting observations from early work with dsDNA using streptavidin as a drag-tag was that the drag induced by including a streptavidin label at both ends was significantly more than double that from a single streptavidin (Heller, C. et al.., J. Chromatogr. A 1998, 806, 113-121). This finding was assumed to be in error, and subsequent work focused on experiments in which only a single drag-tag is appended to one end of the DNA molecule. Recent theoretical work (McCormick, L. C., Slater, G. W., Electrophoresis 2005, 26, 1659-1667) has examined the contribution of end-effects to the free-solution electrophoretic mobility of charged-uncharged polymer conjugates, reopening the question of enhanced drag from placing a drag-tag at both ends. In this study, this effect is investigated experimentally, using custom-synthesized ssDNA oligonucleotides allowing the attachment of drag-tags to one or both ends, as well as dsDNA PCR products generated with primers appropriate for the attachment of drag-tags at one or both ends. A range of sizes of drag-tags are used, including synthetic polypeptoid drag-tags as well as genetically engineered protein polymer drag-tags. The enhanced drag arising from labeling both ends has been confirmed, with 6-9% additional drag for the ssDNA and 10-23% additional drag for the dsDNA arising from labeling both ends than would be expected from simply doubling the size of the drag-tag at one end. The experimental results for ssDNA labeled at both ends are compared to the predictions of the recent theory of end-effects, with reasonably good quantitative agreement. These experimental findings demonstrate the feasibility of enhancing ELFSE separations by labeling both ends of the DNA molecule, leading to greater resolving power and a wider range of applications for this technique.
View details for DOI 10.1002/elps.200500554
View details for Web of Science ID 000237685600003
View details for PubMedID 16645947
A threaded loop conformation adopted by a family of peptoid nonamers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2006; 128 (5): 1733-1738
Non-natural polymers with well-defined three-dimensional folds offer considerable potential for engineering novel functions that are outside the scope of biological polymers. Here we describe a family of N-substituted glycine or "peptoid" nonamers that folds into an unusual "threaded loop" structure of exceptional thermal stability and conformational homogeneity in acetonitrile. The structure is chain-length-specific and relies on bulky, chiral side chains and chain-terminating functional groups for stability. Notable elements of the structure include the engagement of the positively charged amino terminus by carbonyl groups of the backbone through hydrogen bonding interactions and shielding of polar groups from and near-complete exposure of hydrophobic groups to solvent, in a manner resembling a folded polypeptide globular domain turned inside-out. The structure is stable in a variety of organic solvents but is readily denatured in any solvent/cosolvent milieu with hydrogen bonding potential. The structure could serve as a scaffold for the elaboration of novel functions and could be used to test methodologies for predicting solvent-dependent polymer folding.
View details for DOI 10.1021/ja0574318
View details for Web of Science ID 000235224700070
View details for PubMedID 16448149
Chip-based high-sensitivity detection of multiple disease biomarkers
19th IEEE International Conference on Micro Electro Mechanical Systems (MEMS 2006)
IEEE. 2006: 478–481
View details for Web of Science ID 000236994500120
Effect of polymer matrix and glycerol on rapid single-strand conformation polymorphism analysis by capillary and microchip electrophoresis for detection of mutations in K-ras gene
2005; 26 (17): 3380-3386
We present the rapid single-strand conformation polymorphism (SSCP) analysis by capillary and microchip electrophoresis to detect the mutations in K-ras gene. Parameters that might affect the analysis of mutation in K-ras gene, such as the polymer and the additive in the sieving matrix, have been studied systematically. Under the optimal conditions, the analysis of seven mutants of K-ras gene could be finished within 10 min by capillary electrophoresis (CE). Furthermore, with the wild-type gene as the inner standard, the analysis accuracy of mutations could be improved. In addition, by studying the properties of polymer solutions, the matrix suitable for microchip electrophoresis was found, and the detection of mutations in K-ras gene could be further shortened to 1 min.
View details for DOI 10.1002/elps.200500142
View details for Web of Science ID 000231967600020
View details for PubMedID 16097023
Optical monitoring of bubble size and shape in a pulsating bubble surfactometer
JOURNAL OF APPLIED PHYSIOLOGY
2005; 99 (2): 624-633
The pulsating bubble surfactometer (PBS) is often used for in vitro characterization of exogenous lung surfactant replacements and lung surfactant components. However, the commercially available PBS is not able to dynamically track bubble size and shape. The PBS therefore does not account for bubble growth or elliptical bubble shape that frequently occur during device use. More importantly, the oscillatory volume changes of the pulsating bubble are different than those assumed by the software of the commercial unit. This leads to errors in both surface area and surface tension measurements. We have modified a commercial PBS through the addition of an image-acquisition system, allowing real-time determination of bubble size and shape and hence the accurate tracking of surface area and surface tension. Compression-expansion loops obtained with the commercially available PBS software were compared with those provided by the image-analysis system for dipalmitoylphosphatidylcholine, Infasurf, and Tanaka lipids (dipalmitoylphosphatidylcholine-palmitoyloleoylphosphatidyl-glycerol-palmitic acid, 68:22:9) at concentrations of 0.1 and 1.0 mg/ml and at frequencies of 1 and 20 cycles/min. Whereas minimum surface tension as determined by the image-analysis system is similar to that measured by the commercially available software, the maximum surface tension and the shapes of the interfacial area-surface tension loops are quite different. Differences are attributable to bubble drift, nonsinusoidal volume changes, and variable volume excursions seen with the modified system but neglected by the original system. Image analysis reveals that the extent of loop hysteresis is greatly overestimated by the commercial device and that an apparent, rapid increase in surface tension upon film expansion seen in PBS loops is not observed with the image-analysis system. The modified PBS system reveals new dynamic characteristics of lung surfactant preparations that have not previously been reported.
View details for DOI 10.1152/japplphysiol.00748.2004
View details for Web of Science ID 000230486200031
View details for PubMedID 15790687
A modular microfluidic architecture for integrated biochemical analysis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2005; 102 (28): 9745-9750
Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.
View details for DOI 10.1073/pnas.0504082102
View details for Web of Science ID 000230545100004
View details for PubMedID 15985549
Comblike, monodisperse polypeptoid drag-tags for DNA separations by end-labeled free-solution electrophoresis (ELFSE)
2005; 16 (4): 929-938
The development of innovative technologies designed to reduce the cost and increase the throughput of DNA separations continues to be important for large-scale sequencing and genotyping efforts. We report research aimed at the further development of a free-solution bioconjugate method of DNA size separation by capillary electrophoresis (CE), in particular, the determination of an optimal molecular architecture for polyamide-based "drag-tags". We synthesized several branched poly(N-methoxyethyl glycine)s (poly(NMEG)s, a class of polypeptoids) as novel friction-generating entities for end-on attachment to DNA molecules. A 30-mer poly(NMEG) "backbone," comprising five evenly spaced reactive epsilon-amino groups, was synthesized on solid phase, cleaved, and purified to monodispersity by RP-HPLC. Three different comblike derivatives of this backbone molecule were created by (1) acetylating the epsilon-amino groups or (2) appending small, monodisperse NMEG oligomers (a tetramer and an octamer). Grafting of the oligo(NMEG)s was done using solution-phase amide bond formation chemistry. Once purified to total monodispersity, the three different drag-tags were studied by free-solution electrophoresis to observe the effect of branching on their hydrodynamic drag or "alpha" and hence their ability to separate DNA. Drag was found to scale linearly with total molecular weight, regardless of branch length. The octamer-branched drag-tag-DNA conjugate was used to separate ssDNA products of 50, 75, 100, and 150 bases in length by free-solution CE in less than 10 min. Hence, the use of branched or comblike drag-tags is both a feasible and an effective way to achieve high frictional drag, allowing the high-resolution separation of relatively large DNA molecules by free-solution CE without the need to synthesize very long polymers.
View details for DOI 10.1021/bc0496915
View details for Web of Science ID 000230712900021
View details for PubMedID 16029034
New peptidomimetic polymers for antifouling surfaces
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2005; 127 (22): 7972-7973
Exposure of therapeutic and diagnostic medical devices to biological fluids is often accompanied by interfacial adsorption of proteins, cells, and microorganisms. Biofouling of surfaces can lead to compromised device performance or increased cost and in some cases may be life-threatening to the patient. Although numerous antifouling polymer coatings have enjoyed short-term success in preventing protein and cell adsorption on surfaces, none have proven ideal for conferring long-term biofouling resistance. Here we describe a new biomimetic antifouling N-substituted glycine polymer (peptoid) containing a C-terminal peptide anchor derived from residues found in mussel adhesive proteins for robust attachment of the polymer onto surfaces. The methoxyethyl side chain of the peptoid portion of the polymer was chosen for its chemical resemblance to the repeat unit of the known antifouling polymer poly(ethylene glycol) (PEG), whereas the composition of the 5-mer anchoring peptide was chosen to directly mimic the DOPA- and Lys-rich sequence of a known mussel adhesive protein. Surfaces modified with this biomimetic peptide-peptoid conjugate exhibited dramatic reduction of serum protein adsorption and resistance to mammalian cell attachment for over 5 months in an in vitro assay. These new synthetic peptide based antifouling polymers may provide long-term control of surface biofouling in the physiologic, marine, and industrial environments.
View details for DOI 10.1021/jaO522534
View details for Web of Science ID 000229619500005
View details for PubMedID 15926795
Protein polymer drag-tags for DNA separations by end-labeled free-solution electrophoresis
2005; 26 (11): 2138-2148
We demonstrate the feasibility of end-labeled free-solution electrophoresis (ELFSE) separation of DNA using genetically engineered protein polymers as drag-tags. Protein polymers are promising candidates for ELFSE drag-tags because their sequences and lengths are controllable not only to generate monodisperse polymers with high frictional drag, but also to meet other drag-tag requirements for high-resolution separations by microchannel electrophoresis. A series of repetitive polypeptides was designed, expressed in Escherichia coli, and purified. By performing an end-on conjugation of the protein polymers to a fluorescently labeled DNA oligomer (22 bases) and analyzing the electrophoretic mobilities of the conjugate molecules by free-solution capillary electrophoresis (CE), effects of the size and charge of the protein polymer drag-tags were investigated. In addition, the electrophoretic behavior of bioconjugates comprising relatively long DNA fragments (108 and 208 bases) and attached to uncharged drag-tags was observed, by conjugating fluorescently labeled polymerase chain reaction (PCR) products to charge-neutral protein polymers, and analyzing via CE. We calculated the amount of friction generated by the various drag-tags, and estimated the potential read-lengths that could be obtained if these drag-tags were used for DNA sequencing in our current system. The results of these studies indicate that larger and uncharged drag-tags will have the best DNA-resolving capability for ELFSE separations, and that theoretically, up to 233 DNA bases could be sequenced using one of the protein polymer drag-tags we produced, which is electrostatically neutral with a chain length of 337 amino acids. We also show that denatured (unfolded) polypeptide chains impose much greater frictional drag per unit molecular weight than folded proteins, such as streptavidin, which has been used as a drag-tag before.
View details for DOI 10.1002/elps.200410042
View details for Web of Science ID 000229901500009
View details for PubMedID 15880624
Poly(acrylamide-co-alkylacrylamides) for electrophoretic DNA purification in microchannels
2005; 77 (3): 772-779
We have created a family of water-soluble block copolymers of acrylamide and N-alkylacrylamides that are designed to selectively remove proteins from DNA via microchannel electrophoresis. It was hypothesized that the inclusion of hydrophobic subunits in the polymer chain, in sufficient concentration, could lead to protein adsorption due to hydrophobic interactions. A series ofN-alkylacrylamide comonomers with varying alkyl chain lengths (C4, C6, C8) and also an N,N-dialkyl group (C6-C6) were synthesized via reactions between acryloyl chloride and the respective alkylamines. Copolymers were synthesized using an aqueous "micellar" polymerization technique, which involves dissolving acrylamide in the aqueous phase while hydrophobic monomers are solubilized in sodium dodecyl sulfate micelles. Copolymers comprising up to 4 mol % of a hydrophobic subunit (as verified by (1)H NMR) were synthesized. Polymer molecular weights were determined by tandem gel permeation chromatography-multiangle laser light scattering, and ranged from 1.5 x 10(6) to 4.3 x 10(6). Capillary electrophoresis analysis of bovine serum albumin and beta-lactoglobulin migration in these matrixes revealed that the octylacrylamide and dihexylacrylamide copolymers show the most significant extent of protein adsorption while butylacrylamides show no noteworthy adsorption trend. All copolymer matrixes studied allowed the passage of a dsDNA digest, and displayed some DNA sieving ability at 0.5% (w/w) in TTE (50 mM Tris, 50 mM TAPS, 2 mM EDTA, pH 8.4) buffer. These matrixes are demonstrated in on-chip experiments to adsorb protein, in a step toward meeting the front-end processing goals of mu-TAS for genetic analysis applications.
View details for DOI 10.1021/ac049000y
View details for Web of Science ID 000226759000015
View details for PubMedID 15679343
End-labeled free-solution electrophoresis of DNA
2005; 26 (2): 331-350
DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.
View details for DOI 10.1002/elps.200410219
View details for Web of Science ID 000226794400004
View details for PubMedID 15657881
Development of a microfluidic device using nanoparticle-based bio-barcodes for ultrasenstitive detection of proteins
8th International Conference on Miniaturized Systems for Chemistry and Life Sciences
SPRINGER. 2005: 342–44
View details for Web of Science ID 000228997000114
Simple, helical peptoid analogs of lung surfactant protein B
CHEMISTRY & BIOLOGY
2005; 12 (1): 77-88
The helical, amphipathic surfactant protein, SP-B, is a critical element of pulmonary surfactant and hence is an important therapeutic molecule. However, it is difficult to isolate from natural sources in high purity. We have created and studied three different, nonnatural analogs of a bioactive SP-B fragment (SP-B(1-25)), using oligo-N-substituted glycines (peptoids) with simple, repetitive sequences designed to favor the formation of amphiphilic helices. For comparison, a peptide with a similar repetitive sequence previously shown to be a good SP mimic was also studied, along with SP-B(1-25) itself. Surface pressure-area isotherms, surfactant film phase morphology, and dynamic adsorption behavior all indicate that the peptoids are promising mimics of SP-B(1-25). The extent of biomimicry appears to correlate with peptoid helicity and lipophilicity. These biostable oligomers could serve in a synthetic surfactant replacement to treat respiratory distress syndrome.
View details for DOI 10.1016/j.chembiol.2004.10.014
View details for Web of Science ID 000226798200012
View details for PubMedID 15664517
DNA sequencing and genotyping in miniaturized electrophoresis systems
2004; 25 (21-22): 3564-3588
Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.
View details for DOI 10.1002/elps.200406161
View details for Web of Science ID 000225679000008
View details for PubMedID 15565709
Sparsely cross-linked "nanogel" matrixes as fluid, mechanically stabilized polymer networks for high-throughput microchannel DNA sequencing
2004; 76 (18): 5249-5256
We have developed sparsely cross-linked "nanogels", subcolloidal polymer structures composed of covalently linked, linear polyacrylamide chains, as novel replaceable DNA sequencing matrixes for capillary and microchip electrophoresis. Nanogels were synthesized via inverse emulsion (water-in-oil) copolymerization of acrylamide and a low percentage (approximately 10(-4) mol %) of N,N-methylene bisacrylamide (Bis). Nanogels and nanogel networks were characterized by multiangle laser light scattering and rheometry, respectively, and tested for DNA sequencing in both capillaries and chips with four-color LIF detection. Typical nanogels have an average radius of approximately 230 nm, with approximately 75% of chains incorporating a Bis cross-linker. The properties and performance of nanogel matrixes are compared here to those of a linear polyacrylamide (LPA) network, matched for both polymer weight-average molar mass (M(w)) and the extent of interchain entanglements (c/c). At sequencing concentrations, the two matrixes have similar flow characteristics, important for capillary and microchip loading. However, because of the physical network stability provided by the internally cross-linked structure of the nanogels, substantially longer average read lengths are obtained under standard conditions with the nanogel matrix at a 98.5% accuracy of base-calling (for CE: 680 bases, an 18.7% improvement over LPA, with the best reads as long as 726 bases, compared to 568 bases for the LPA matrix). We further investigated the use of the nanogel matrixes in a high-throughput microfabricated DNA sequencing device consists of 96 separation channels densely fabricated on a 6-in. glass wafer. Again, preliminary DNA sequencing results show that the nanogel matrixes are capable of delivering significantly longer average read length, compared to an LPA matrix of comparable properties. Moreover, nanogel matrixes require 30% less polymer per unit volume than LPA. The addition of a small amount of low molar mass LPA or ultrahigh molar mass LPA to the optimized nanogel sequencing matrix further improves read length as well as the reproducibility of read length (RSD < 1.6%). This is the first report of a replaceable DNA sequencing matrix that provides better performance than LPA, in a side-by-side comparison of polymer matrixes appropriately matched for molar mass and the extent of interchain entanglements. These results could have significant implications for the improvement of microchip-based DNA sequencing technology.
View details for DOI 10.1021/ac049721x
View details for Web of Science ID 000223928800002
View details for PubMedID 15362880
Thermoresponsive N,N-dialkylacrylamide copolymer blends as DNA sieving matrices with a thermally tunable mesh size
2004; 25 (7-8): 1007-1015
In an earlier study we showed that a blend of thermoresponsive and nonthermoresponsive hydroxyalkylcelluloses could be used to create a thermally tunable polymer network for double-stranded (ds) DNA separation. Here, we show the generality of this approach using a family of polymers suited to a wider range of DNA separations: a blended mixture of N,N-dialkylacrylamide copolymers with different thermoresponsive behaviors. A mixture of 47% w/w N,N-diethylacrylamide (DEA)/53% w/w N,N-dimethylacrylamide (DMA) (DEA47; thermoresponsive, transition temperature = 55 degrees C in water) and 30% w/w DEA/70% w/w DMA (DEA30; nonthermoresponsive, transition temperature > 85 degrees C in water) copolymers in the ratio of 1:5 w/w DEA47:DEA30 was used to separate a dsDNA restriction digest (PhiX174-HaeIII). We investigated the effects of changing mesh size on dsDNA separation, as controlled by temperature. We observed good DNA separation performance with the copolymer blend at temperatures ranging from 25 degrees C to 48 degrees C. The separation selectivity was evaluated quantitatively for certain DNA fragment pairs as a function of temperature. The results were compared with those obtained with a control matrix consisting only of the nonthermoresponsive DEA30. Different DNA fragment pairs of various sizes show distinct temperature-dependent selectivities. Over the same temperature range, no significant temperature dependence of selectivity is observed for these DNA fragment pairs in the nonthermoresponsive control matrix. Overall, the results show similar trends in the temperature dependency of separation selectivity to what was previously observed in hydroxyalkylcellulose blends, for the same DNA fragment pairs. Finally, we showed that a ramped temperature scheme enables improved separation in the blended copolymer matrix for both small and large DNA fragments, simultaneously in a single capillary electrophoresis (CE) run.
View details for DOI 10.1002/elps.200305785
View details for Web of Science ID 000221168700010
View details for PubMedID 15095441
Characterization of glutamine deamidation in a long, repetitive protein polymer via bioconjugate capillary electrophoresis
2004; 5 (2): 618-627
We describe a novel method for the determination of glutamine deamidation in a long protein polymer via bioconjugate capillary electrophoresis. Since the current best technique for detection of glutamine (or asparagine) deamidation is mass spectrometry, it is practically impossible to precisely detect the degree of deamidation (i.e., how many residues are deamidated in a polypeptide) in a large protein containing a significant number of glutamine (or asparagine) residues, because the mass difference between native and deamidated residues is just 1 atomic mass unit. However, by covalently attaching polydisperse protein polymers (337 residues) to a monodisperse DNA oligomer (22 bases), the degree of glutamine deamidation, which could not be determined accurately by mass spectrometry, was resolved by free-solution capillary electrophoresis. Electrophoretic separations were carried out after different durations of exposure of the protein to a cyanogen bromide cleavage reaction mixture, which is a general treatment for the purpose of removing an oligopeptide affinity purification tag from fusion proteins. For protein polymers with increasing extents of deamidation, the electromotive force of DNA + polypeptide conjugate molecules increases due to the introduced negative charge of deamidated glutamic acid residues, and consequently CE analysis reveals increasing differences in the electrophoretic mobilities of conjugate molecules, which qualitatively shows the degree of deamidation. Peak analysis of the electropherograms enables quantitative determination of the first four deamidations in a protein polymer. A first-order rate constant of 0.018 h(-1) was determined for the deamidation of a single glutamine residue in the protein polymer during the cyanogen bromide cleavage reaction.
View details for DOI 10.1021/bm034442p
View details for Web of Science ID 000220109200049
View details for PubMedID 15003029
- Flow-induced chain scission as a physical route to narrowly distributed, high molar mass polymers POLYMER 2004; 45 (4): 1223-1234
A very thin coating for capillary zone electrophoresis of proteins based on a tri(ethylene glycol)-terminated alkyltrichlorosilane
2004; 25 (3): 405-414
We describe the use of a tri(ethylene glycol)-terminated alkyltrichlorosilane to create a very thin, protein-resistant "self-assembled monolayer" coating on the inner surface of a fused-silica capillary. The same compound has been demonstrated previously on flat silica substrates to resist adsorption of many proteins. As a covalently bound capillary coating, it displays good resistance to the adsorption of cationic proteins, providing clean separations of a mixture of lysozyme, cytochrome c, ribonuclease A, and myoglobin for more than 200 consecutive runs. Electroosmotic flow (EOF) was measured as a function of pH; the coated capillary retains significant cathodal EOF, with roughly 50% of the EOF of an uncoated capillary at neutral pH, making this coating promising for applications requiring some EOF. The EOF was reasonably stable, with a 2.9% relative standard deviation during a 24 h period consisting of 72 consecutive separations of cationic proteins. Efficiencies for cationic protein separations were moderate, in the range of 190,000-290,000 theoretical plates per meter. The coating procedure was simple, requiring only a standard cleaning procedure followed by a rinse with the silane reagent at room temperature. No buffer additives are required to maintain the stability of the coating, making it flexible for a range of applications, potentially including capillary electrophoresis-mass spectrometry (CE-MS).
View details for DOI 10.1002/elps.200305714
View details for Web of Science ID 000188996900003
View details for PubMedID 14760631
A novel thermogelling matrix for microchannel DNA sequencing based on poly-N-alkoxyalkylacrylamide copolymers
2003; 24 (24): 4161-4169
We have developed a novel class of thermogelling polymer networks based on poly-N-alkoxyalkylacrylamides, and demonstrated their use as DNA sequencing matrices for high-throughput microchannel electrophoresis in capillary arrays. Polymers and copolymers of N-ethoxyethylacrylamide (NEEA) and N-methoxyethylacrylamide (NMEA) were synthesized by aqueous-phase free-radical polymerization and characterized by tandem gel permeation chromatography-multi-angle laser light scattering. These copolymer matrices exhibit "re-entrant"-type volume phase transitions, forming entangled networks with high shear viscosity at low (< 20 degrees C) and high (> 35 degrees C) temperatures, and undergoing a "coil-to-globular", lower critical solution temperature (LCST)-like phase transition over an intermediate temperature range (20-35 degrees C). Hence, matrix viscosity is relatively low at room temperature (25 degrees C), and increases rapidly above 35 degrees C. The material properties and phase behavior of these thermogelling polymer networks were studied by steady-shear rheometry. These matrices are easily loaded into capillary arrays at room temperature while existing as viscous fluids, but thermogel above 35 degrees C to form transparent hydrogels via a thermo-associative phase transition. The extent of the intermediate viscosity drop and the final viscosity increase depends on the composition of the copolymers. DNA sequencing by capillary array electrophoresis with four-color laser-induced fluorescence (LIF) detection shows that these thermogelling networks provide enhanced resolution of both small and large DNA sequencing fragments and longer sequencing read lengths, in comparison to appropriate control (closely related, nonthermogelling) polymer networks. In particular, a copolymer comprised of 90% w/w NMEA and 10% w/w NEEA, with a molecular mass of approximately 2 MDa, delivers around 600 bases at 98.5% base-calling accuracy in 100 min of electrophoresis.
View details for DOI 10.1002/elps.200305670
View details for Web of Science ID 000187897300002
View details for PubMedID 14679563
Sparsely cross-linked "nanogels" for microchannel DNA sequencing
2003; 24 (24): 4170-4180
We have developed sparsely cross-linked "nanogels", sub-colloidal polymer structures composed of covalently linked, linear polyacrylamide chains, as novel DNA sequencing matrices for capillary electrophoresis. The presence of covalent cross-links affords nanogel matrices with enhanced network stability relative to standard, linear polyacrylamide (LPA), improving the separation of large DNA fragments. Nanogels were synthesized via inverse emulsion (water-in-oil) copolymerization of acrylamide and N,N-methylenebisacrylamide (Bis). In order to retain the fluidity necessary in a replaceable polymer matrix for capillary array electrophoresis (CAE), a low percentage of the Bis cross-linker (< 10(-4) mol%) was used. Nanogels were characterized by multiangle laser light scattering and rheometry, and were tested for DNA sequencing by CAE with four-color laser-induced fluorescence (LIF) detection. The properties and performance of nanogel matrices were compared to those of a commercially available LPA network, which was matched for both weight-average molar mass (Mw) and extent of interchain entanglements (c/c*). Nanogels presented in this work have an average radius of gyration of 226 nm and a weight-average molar mass of 8.8 x 10(6) g/mol. At concentrations above the overlap threshold, nanogels form a clear, viscous solution, similar to the LPA matrix (Mw approximately 8.9 x 10(6) g/mol). The two matrices have similar flow and viscosity characteristics. However, because of the physical network stability provided by the internally cross-linked structure of the nanogels, a substantially longer read length ( approximately 63 bases, a 10.4% improvement) is obtained with the nanogel matrix at 98.5% accuracy of base-calling. The nanogel network provides higher-selectivity separation of ssDNA sequencing fragments longer than 375 bases. Moreover, nanogel matrices require 30% less polymer per unit volume than LPA. This is the first report of a sequencing matrix that provides better performance than LPA, in a side-by-side comparison of polymer matrices matched for Mw and extent of interchain entanglements.
View details for DOI 10.1002/elps.200305702
View details for Web of Science ID 000187897300003
View details for PubMedID 14679564
Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2003; 125 (44): 13525-13530
Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.
View details for DOI 10.1021/ja037540r
View details for Web of Science ID 000186289300054
View details for PubMedID 14583049
Helical peptoid mimics of lung surfactant protein C
CHEMISTRY & BIOLOGY
2003; 10 (11): 1057-1063
Among the families of peptidomimetic foldamers under development as novel biomaterials and therapeutics, poly-N-substituted glycines (peptoids) with alpha-chiral side chains are of particular interest for their ability to adopt stable, helical secondary structure in organic and aqueous solution. Here, we show that a peptoid 22-mer with a biomimetic sequence of side chains and an amphipathic, helical secondary structure acts as an excellent mimic of surfactant protein C (SP-C), a small protein that plays an important role in surfactant replacement therapy for the treatment of neonatal respiratory distress syndrome. When integrated into a lipid film, the helical peptoid SP mimic captures the essential surface-active behaviors of the natural protein. This work provides an example of how an abiological oligomer that closely mimics both the hydrophobic/polar sequence patterning and the fold of a natural protein can also mimic its biophysical function.
View details for DOI 10.1016/j.chembiol.2003.10.008
View details for Web of Science ID 000186858600008
View details for PubMedID 14652073
Helical peptoid mimics of magainin-2 amide
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2003; 125 (40): 12092-12093
A series of peptoid oligomers were designed as helical, cationic, and facially amphipathic mimics of the magainin-2 amide antibacterial peptide. We used circular dichroism spectroscopy to determine the conformation of these peptoids in aqueous buffer and in the presence of bacterial membrane-mimetic lipid vesicles, composed of a 7:3 mol ratio of POPE:POPG. We found that certain peptoids, which displayed characteristically helical CD in buffer and lipid vesicles, exhibit selective (nonhemolytic) and potent antibacterial activity against both Gram-positive and Gram-negative bacteria. In contrast, peptoids that exhibit weak CD, reminiscent of that of a peptide random coil, were ineffective antibiotics. In a manner similar to the natural magainin peptides, we find a correlation between peptoid lipophilicity and hemolytic propensity. We observe that a minimum length of approximately 12 peptoid residues may be required for antibacterial activity. We also see evidence that a helix length between 24 and 34 A may provide optimal antibacterial efficacy. These results provide the first example of a water-soluble, structured, bioactive peptoid.
View details for DOI 10.1021/ja037320d
View details for Web of Science ID 000185784700016
View details for PubMedID 14518985
Tandem isotachophoresis-zone electrophoresis via base-mediated destacking for increased detection sensitivity in microfluidic systems
2003; 75 (13): 3059-3065
Electrophoresis in microfluidic devices is becoming a useful analytical platform for a variety of biological assays. In this report, we present a method that allows for an increased sensitivity of detection of fluorescent molecules in microfluidic electrophoresis devices. This capability is provided by the implementation of a particular buffer system that is designed to initially function in an isotachophoretic (ITP) mode and, then after a controlled amount of electric current has been applied to the system, to transition to a zone electrophoretic mode. In the initial ITP mode, analytes dissolved in a large volume of injected sample are concentrated into a single narrow zone. After application of a sufficient and adjustable amount of electric current, the system switches into a zone electrophoretic mode, where the concentrated analytes are separated according to their electrophoretic mobilities. Application of this tandem ITP-zone electrophoretic strategy to the concentration, separation, and detection of fluorescent reporter molecules in a standard microfluidic device results in an approximately 50-fold increase in detection sensitivity relative to equivalent separations that are obtained with zone electrophoresis alone. Even with very long initial sample plugs (up to 3000 microm), this strategy produces electrophoretic separations with high resolutions and peak efficiencies. This strategy can be implemented to increase detection sensitivity in any standard microfluidic electrophoresis platform and does not require any specialized hardware or microchannel configurations.
View details for DOI 10.1021/ac0259921
View details for Web of Science ID 000183975300022
View details for PubMedID 12964751
Poly-N-hydroxyethylacrylamide as a novel, adsorbed coating for protein separation by capillary electrophoresis
2003; 24 (7-8): 1166-1175
We present the polymer poly-N-hydroxyethylacrylamide (PHEA) (polyDuramide) as a novel, hydrophilic, adsorbed capillary coating for electrophoretic protein analysis. Preparation of the PHEA coating requires a simple and fast (30 min) protocol that can be easily automated in capillary electrophoresis instruments. Over the pH range of 3-8.4, the PHEA coating is shown to reduce electroosmotic flow (EOF) by about 2 orders of magnitude compared to the bare silica capillary. In a systematic comparative study, the adsorbed PHEA coating exhibited minimal interactions with both acidic and basic proteins, providing efficient protein separations with excellent reproducibility on par with a covalent polyacrylamide coating. Hydrophobic interactions between proteins and a relatively hydrophobic poly-N,N-dimethylacrylamide (PDMA) adsorbed coating, on the other hand, adversely affected separation reproducibility and efficiency. Under both acidic and basic buffer conditions, the adsorbed PHEA coating produced an EOF suppression performance comparable to that of covalent polyacrylamide coating and superior to that of adsorbed PDMA coating. The protein separation performance in PHEA-coated capillaries was retained for 275 consecutive protein separation runs at pH 8.4, and for more than 800 runs at pH 4.4. The unique and novel combination of hydrophilicity and adsorptive coating ability of PHEA makes it a suitable wall coating for automated microscale analysis of proteins by capillary array systems.
View details for Web of Science ID 000182693400005
View details for PubMedID 12707908
Detection of Escherichia coli O157 : H7 bacteria by a combination of immunofluorescent staining and capillary electrophoresis
2003; 24 (4): 655-661
As the number of incidents of bacterial infections continues to rise around the globe, simpler, faster, and more sensitive diagnostic techniques are required to improve the safety of the food supply and to screen for potential bacterial infections in humans. We present here direct and indirect approaches for the detection of bacteria, which are based upon a combination of immunofluorescent staining and capillary electrophoresis. In the direct approach, Escherichia coli O157:H7 bacteria stained with fluorescein-tagged specific antibodies are detected by CE, while in the indirect approach fluorescein-tagged specific antibodies to E. coli are first captured by E. coli O157:H7 bacteria and then released and detected by CE. We have identified suitable bacteria staining and CE protocols, which involved a 10 mM Tris-borate-EDTA (TBE) buffer, 0.25 micro g antibody/1 million bacteria, and capillaries dynamically coated with poly-N-hydroxyethylacrylamide (polyDuramide). We have also successfully detected the presence of E. coli O157:H7 in contaminated meat. The total time required for analysis was 6-8 h, which is less than that realized in most commercial assays presently available.
View details for Web of Science ID 000181507200011
View details for PubMedID 12601734
Microchannel wall coatings for protein separations by capillary and chip electrophoresis
16th International Symposium on Microscale Separation and Analysis
WILEY-BLACKWELL. 2003: 34–54
The necessity for microchannel wall coatings in capillary and chip-based electrophoretic analysis of biomolecules is well understood. The regulation or elimination of EOF and the prevention of analyte adsorption is essential for the rapid, efficient separation of proteins and DNA within microchannels. Microchannel wall coatings and other wall modifications are especially critical for protein separations, both in fused-silica capillaries, and in glass or polymeric microfluidic devices. In this review, we present a discussion of recent advances in microchannel wall coatings of three major classes--covalently linked polymeric coatings, physically adsorbed polymeric coatings, and small molecule additives. We also briefly review modifications useful for polymeric microfluidic devices. Within each category of wall coatings, we discuss those used to eliminate EOF, to tune EOF, to prevent analyte adsorption, or to perform multiple functions. The knowledgeable application of the most promising recent developments in this area will allow for the separation of complex protein mixtures and for the development of novel microchannel wall modifications.
View details for Web of Science ID 000180637300006
View details for PubMedID 12652571
A DNA sieving matrix with thermally tunable mesh size
16th International Symposium on Microscale Separation and Analysis
WILEY-BLACKWELL. 2003: 55–62
We present a "proof-of-concept" study showing that a blend of thermo-responsive and nonthermo-responsive polymers can be used to create a DNA sieving matrix with a thermally tunable mesh size, or "dynamic porosity". Various blends of two well-studied sieving polymers for CE, including hydroxypropylcellulose (HPC), a thermo-responsive polymer, and hydroxyethylcellulose (HEC), a nonthermo-responsive polymer, were used to separate a double-stranded DNA restriction digest (Phi X174-HaeIII). HPC exhibits a volume-phase transition in aqueous solution which results in a collapse in polymer coil volume at approximately 39 degrees C. Utilizing a blend of HPC and HEC in a ratio of 1:5 by weight, we investigated the effects of changing mesh size on DNA separation, as controlled by temperature. High-resolution DNA separations were obtained with the blended matrix at temperatures ranging from 25 degrees C to 38 degrees C. We evaluated changes in the selectivity of DNA separation with increasing temperature for certain pairs of small and large fragments. A pure HEC (nonthermo-responsive) matrix was used over the same temperature range as a negative control. In the blended matrix, we observe a maximum in selectivity at approximately 31 degrees C for small DNA, while a significant increase in the selectivity of large-DNA separation occurs at approximately 36 degrees C as the polymer mesh "opens". We also demonstrate, through a temperature ramping experiment, that this matrix can be utilized to obtain high-resolution separation of both small and large DNA fragments simultaneously in a single CE run. Blended polymer matrices with "dynamic porosity" have the potential to provide enhanced genomic analysis by capillary array or microchip electrophoresis in microfluidic devices with advanced temperature control.
View details for Web of Science ID 000180637300007
View details for PubMedID 12652572
Mimicry of bioactive peptides via non-natural, sequence-specific peptidomimetic oligomers
CURRENT OPINION IN CHEMICAL BIOLOGY
2002; 6 (6): 872-877
Non-natural, sequence-specific peptidomimetic oligomers are being designed to mimic bioactive peptides, with potential therapeutic application. Cationic, facially amphipathic helical beta-peptide oligomers have been developed as magainin mimetics. Non-natural mimics of HIV-Tat protein, lung surfactant proteins, collagen, and somatostatin are also being developed. Pseudo-tertiary structure in beta-peptides and peptoids may herald the creation of entirely artificial proteins.
View details for DOI 10.1016/S1367-5931(02)00385-X
View details for Web of Science ID 000179638400023
View details for PubMedID 12470744
A new cloning method for the preparation of long repetitive polypeptides without a sequence requirement
2002; 35 (22): 8281-8287
View details for Web of Science ID 000178738000008
Multiplexed, high-throughput genotyping by single-base extension and end-labeled free-solution electrophoresis
2002; 74 (17): 4328-4333
Technologies that allow for high-throughput, economical, and accurate single nucleotide polymorphism (SNP) genotyping are becoming crucial for modern genomic efforts. Here, we present a method for multiplexed single-base extension (SBE) genotyping that takes advantage of the unique separation modalities made possible via end-labeled free-solution electrophoresis (ELFSE). Three unique SBE oligonucleotide primers, which probe for mutations of clinical importance in the human p53 gene, were covalently conjugated to three unique polypeptoid frictional end labels and mixed together. This primer-polypeptoid conjugate cocktail was then used in a multiplexed SBE reaction followed by free-solution separation in a 96-capillary array electrophoresis (CAE) instrument. The study was designed to demonstrate multiplexed SNP genotyping of several loci in a single reaction and a single subsequent analysis. Further, the electrophoretic analysis was conducted without any viscous polymeric separation media, was complete in less than 10 min, and can be implemented in any capillary or microfluidic electrophoretic system with four-color fluorescent detection capabilities. Multiplexed SBE-ELFSE genotyping analysis resulted in the simultaneous and accurate genotyping of three p53 loci on five different DNA templates in a single reaction set and single CAE analysis. With the implementation of this method in 96 or more capillaries in parallel, high-throughput screening of SNPs will be accessible to a large number of laboratories.
View details for DOI 10.1021/ac0258094
View details for Web of Science ID 000177862800008
View details for PubMedID 12236339
Critical factors for high-performance physically adsorbed (dynamic) polymeric wall coatings for capillary electrophoresis of DNA
2002; 23 (16): 2766-2776
Physically adsorbed (dynamic) polymeric wall coatings for microchannel electrophoresis have distinct advantages over covalently linked coatings. In order to determine the critical factors that control the formation of dynamic wall coatings, we have created a set of model polymers and copolymers based on N,N-dimethylacrylamide (DMA) and N,N-diethylacrylamide (DEA), and studied their adsorption behavior from aqueous solution as well as their performance for microchannel electrophoresis of DNA. This study is revealing in terms of the polymer properties that help create an "ideal" wall coating. Our measurements indicate that the chemical nature of the coating polymer strongly impacts its electroosmotic flow (EOF) suppression capabilities. Additionally, we find that a critical polymer chain length is required for polymers of this type to perform effectively as microchannel wall coatings. The effective mobilities of double-stranded (dsDNA) fragments within dynamically coated capillaries were determined in order to correlate polymer hydrophobicity with separation performance. Even for dsDNA, which is not expected to be a strongly adsorbing analyte, wall coating hydrophobicity has a deleterious influence on separation performance.
View details for Web of Science ID 000177888500025
View details for PubMedID 12210181
Optimized sample preparation for tandem capillary electrophoresis single-stranded conformational polymorphism/heteroduplex analysis
2002; 33 (2): 318-?
Here we describe DNA sample preparation methods that allow the rapid, simultaneous generation of both single-stranded conformational polymorphism (SSCP) and heteroduplex DNA elements from a single sample in a single tube, which are suitable for direct injection into a capillary electrophoresis (CE) instrument with excellent sensitivity of genetic mutation detection. The p53 gene was used as a model DNA region for this study, which was performed on a high-throughput MegaBACE 96-capillary array electrophoresis instrument. We found that, contrary to the practice common in slab-gel SSCP analysis, denaturants such as formamide are incompatible with this novel technique because they result in homo- and heteroduplex peak broadening in CE (possibly as a result of incomplete dsDNA re-hybridization) that reduces the peak resolution and hence the sensitivity of mutation detection. We also have found that PCR buffers, which are typically used to suspend samples for slab-gel heteroduplex analysis (HA), but which are less suitable for CE because of the presence of extra salt that reduces the efficiency of electrokinetic injection, may be substituted with a 10 mM Tris-HCI buffer (pH 8.5). The use of this Tris-HCl buffer for sample preparation provides both a high sensitivity of mutation detection by tandem SSCP/HA and high efficiency ofelectrokinetic injection by CE. In a related study (published elsewhere), we have applied this optimized protocol to the screening of a set of 32 mutant DNA samples from p53 exons 7 and 8 and recorded 100% sensitivity of mutation detection for tandem CE-SSCP/HA, whereas each individual method yielded lower sensitivity on its own (93% for SSCP and 75% for HA).
View details for Web of Science ID 000177416600014
View details for PubMedID 12188184
In situ crosslinking of a biomimetic peptide-PEG hydrogel via thermally triggered activation of factor XIII
2002; 23 (13): 2703-2710
There is a medical need for robust, biocompatible hydrogels that can be rapidly crosslinked in situ through the use of gentle and non-toxic triggers, which could be used as a surgical adhesive, a bone-inductive material, or for drug and gene delivery. The complete gelation system described here includes calcium-loaded liposomes, hrFactor XIII. thrombin, and an enzymatic substrate based on a four-armed PEG in which each arm terminates with a 20mer peptide sequence derived from the gamma-chain of fibrin. Controlled release of calcium ions for efficient hrFXIII activation was accomplished by thermal triggering of a tailored liposome phase transition at 37 degrees C, which allowed the entire gelation system to be stored in aqueous solution at room temperature without premature gelation. When the system temperature was raised to 37 degrees C (body temperature), the released calcium activates the hrFactor XIII, and gelation was observed to occur within 9 min. Rheological studies performed to quantitatively determine the storage modulus (G') of the gel during oscillatory shear show that it behaves as a robust, elastic solid. Scanning electron microscopy studies revealed the hydrogel to have a very dense morphology overall, however spherical voids are observed in regions where calcium-loaded liposomes were entrapped during gelation.
View details for Web of Science ID 000175718600009
View details for PubMedID 12059019
High-throughput, high-sensitivity genetic mutation detection by tandem single-strand conformation polymorphism/heteroduplex analysis capillary array electrophoresis
2002; 74 (11): 2565-2572
We present the first optimization of linear polyacrylamide (LPA)-based DNA separation matrixes for an automated tandem microchannel single-strand conformation polymorphism (SSCP)/heteroduplex analysis (HA) method, implemented in capillary arrays dynamically coated with poly(N-hydroxyethylacrylamide) (polyDuramide). An optimized protocol for sample preparation allowed both SSCP and HA species to be produced in one step in a single tube and distinguished in a single electrophoretic analysis. A simple, two-color fluorescent sample labeling and detection strategy enabled unambiguous identification of all DNA species in the electropherogram, both single- and double-stranded. Using these protocols and a panel of 11 p53 mutant DNA samples in comparison with wild-type, we employed high-throughput capillary array electrophoresis (CAE) to carry out a systematic and simultaneous optimization of LPA weight-average molar mass (Mw) and concentration for SSCP/HA peak separation. The combination of the optimized LPA matrix (6% LPA, Mw 600 kDa) and a hydrophilic, adsorbed polyDuramide wall coating was found to be essential for resolution of CAE-SSCP/HA peaks and yielded sensitive mutation detection in all 11 p53 samples initially studied. A larger set of 32 mutant DNA specimens was then analyzed using these optimized tandem CAE-SSCP/HA protocols and materials and yielded 100% sensitivity of mutation detection, whereas each individual method yielded lower sensitivity on its own (93% for SSCP and 75% for HA). This simple, highly sensitive tandem SSCP/HA mutation detection method should be easily translatable to electrophoretic analyses on microfluidic devices, due to the ease of the capillary coating protocol and the low viscosity of the matrix.
View details for DOI 10.1021/ac020025b
View details for Web of Science ID 000175995400024
View details for PubMedID 12069238
DNA sequencing with hydrophilic and hydrophobic polymers at elevated column temperatures
2002; 23 (10): 1421-1428
Read length in DNA sequencing by capillary electrophoresis at elevated temperatures is shown to be greatly affected by the extent of hydrophobicity of the polymer separation matrix. At column temperatures of up to 80 degrees C, hydrophilic linear polyacrylamide (LPA) provides superior read length and separation speed compared to poly(N,N-dimethylacrylamide) (PDMA) and a 70:30 copolymer of N,N-dimethylacrylamide and N,N-diethylacrylamide (PDEA30). DNA-polymer and polymer intramolecular interactions are presumed to be a major cause of band broadening and the subsequent loss of separation efficiency with the more hydrophobic polymers at higher column temperatures. With LPA, these interactions were reduced, and a read length of 1000 bases at an optimum temperature of 70 degrees -75 degrees C was achieved in less than 59 min. By comparison, PDMA produced a read length of roughly 800 bases at 50 degrees C, which was close to the read length attained in LPA at the same temperature; however, the migration time was approximately 20% longer, mainly because of the higher polymer concentration required. At 60 degrees C, the maximum read length was 850 bases for PDMA, while at higher temperatures, read lengths for this polymer were substantially lower. With the copolymer DEA30, read length was 650 bases at the optimum temperature of 50 degrees C. Molecular masses of these polymers were determined by tandem gel permeation chromatography-multiangle laser light scattering method (GPC-MALLS). The results indicate that for long read, rapid DNA sequencing and analysis, hydrophilic polymers such as LPA provide the best overall performance.
View details for Web of Science ID 000175992800008
View details for PubMedID 12116152
Capillary array electrophoresis.
2002; 23 (10): 1360-?
View details for PubMedID 12116145
Microchannel DNA sequencing matrices with switchable viscosities
2002; 23 (10): 1398-1409
We review the variety of thermo-responsive and shear-responsive polymer solutions with "switchable" viscosities that have been proposed for application as DNA sequencing matrices for capillary and microfluidic chip electrophoresis. Generally, highly entangled polymer solutions of high-molar mass polymers are necessary for the attainment of long DNA sequencing read lengths (> 500 bases) with short analysis times (< 3 h). However, these entangled polymer matrices create practical difficulties for microchannel electrophoresis with their extremely high viscosities, necessitating high-pressure loading into capillaries or chips. Shear-responsive (shear-thinning) polymer matrices exhibit a rapid drop in viscosity as the applied shear force is increased, but still require a high initial pressure to initiate flow of the solution into a microchannel. Polymer matrices designed to have thermo-responsive properties display either a lowered (thermo-thinning) or raised (thermo-thickening) viscosity as the temperature of the solution is elevated. These properties are generally designed into the polymers by the incorporation of moderately hydrophobic groups in some part of the polymer structure, which either phase-separate or hydrophobically aggregate at higher temperatures. In their low-viscosity states, these matrices that allow rapid loading of capillary or chip microchannels under low applied pressure. The primary goal of work in this area is to design polymer matrices that exhibit this responsive behavior and hence easy microchannel loading, without a reduction in DNA separation performance compared to conventional matrices. While good progress has been made, thermo-responsive matrices have yet to offer sequencing performance as good as nonthermo-responsive networks. The challenge remains to accomplish this goal through the innovative design of novel polymer structures.
View details for Web of Science ID 000175992800005
View details for PubMedID 12116149
Technical challenges in applying capillary electrophoresis-single strand conformation polymorphism for routine genetic analysis
2002; 23 (10): 1375-1385
Recent and future advances in population genetics will have a significant impact on health care practices and the economics of health care provision only if a spectrum of patient-tailored, effective methods of DNA screening for sequence alterations has been developed. Genetic screening by capillary electrophoresis-single strand conformation polymorphism (CE-SSCP), which is based upon the differences in electrophoretic mobilities of wild-type and mutant DNA species, offers an important complement to other presently available techniques such as Sanger sequencing and DNA hybridization arrays due to its simplicity, versatility, and low cost of analysis. A two-part review of CE-SSCP that discusses its advantages and limitations is presented. Emphasis is placed on technological aspects of CE-SSCP (including such rarely addressed issues as sample preparation protocols and the nature of the polymeric DNA separation matrix) as well as on the potential of CE-SSCP for routine genetic analysis. An attempt is made to organize and present the information in sufficient detail to allow the use of SSCP for routine genetic screening even by those inexperienced in CE. Some discussion of CE-based heteroduplex analysis (HA) is also presented.
View details for Web of Science ID 000175992800003
View details for PubMedID 12116147
Poly-N-hydroxyethylacrylamide (polyDuramide (TM)): A novel, hydrophilic, self-coating polymer matrix for DNA sequencing by capillary electrophoresis
2002; 23 (10): 1429-1440
A replaceable polymer matrix, based on the novel monomer N-hydroxyethylacrylamide (HEA), has been synthesized for application in DNA separation by microchannel electrophoresis. The monomer was found by micellar electrokinetic chromatography analysis of monomer partitioning between water and 1-octanol to be more hydrophilic than acrylamide and N,N-dimethylacrylamide. Polymers were synthesized by free radical polymerization in aqueous solution. The weight-average molar mass of purified polymer was characterized by tandem gel permeation chromatography-multiangle laser light scattering. The steady-shear rheological behavior of the novel DNA sequencing matrix was also characterized, and it was found that the viscosity of the novel matrix decreases by more than 2 orders of magnitude as the shear rate is increased from 0.1 to 1000 s(-1). Moreover, in the shear-thinning region, the rate of change of matrix viscosity with shear rate increases with increasing polymer concentration. Poly-N-hydroxyethylacrylamide (PHEA) exhibits good capillary-coating ability, via adsorption from aqueous solution, efficiently suppressing electroosmotic flow (EOF) in a manner comparable to that of poly-N,N-dimethylacrylamide. Under DNA sequencing conditions, adsorptive PHEA coatings proved to be stable and to maintain negligible EOF for over 600 h of electrophoresis. Resolution of DNA sequencing fragments, particularly fragments > 500 bases, in PHEA matrices generally improves with increasing polymer concentration and decreasing electric field strength. When PHEA is used both as a separation matrix and as a dynamic coating in bare silica capillaries, the matrix can resolve over 620 bases of contiguous DNA sequence within 3 h. These results demonstrate the good potential of PHEA matrices for high-throughput DNA analysis by microchannel electrophoresis.
View details for Web of Science ID 000175992800009
View details for PubMedID 12116153
Profiling solid-phase synthesis products by free-solution conjugate capillary electrophoresis
2002; 13 (3): 663-670
Solid-phase synthesis of oligomers, both natural and nonnatural, has proved to be invaluable for the development of many areas of biotechnology. A critical step in the solid-phase synthesis of any oligomer is determining the number and concentration of different constituents present in the product mixture resulting from the synthesis, both before and after purification. Most typically, this analysis is performed by reversed-phase high performance liquid chromatography (RP-HPLC), with the separated components detected by UV absorbance. Recently, we described a novel technique, free-solution conjugate electrophoresis (FSCE), for the high-resolution separation and sensitive laser-induced fluorescence (LIF) detection of uncharged, synthetic polymers, PEG in particular. In this report, we apply this bioconjugate capillary electrophoresis technique to analyze products of the solid-phase synthesis of oligomeric polyamides, namely poly(N-substituted glycines), or polypeptoids. When compared to more traditional RP-HPLC analysis, FSCE analysis of oligomeric peptoids results in separation resolutions that are approximately five times higher and separation efficiencies that are increased by 150%. Moreover, when FSCE with LIF detection is applied to the analysis of oligomeric polyamides after HPLC purification, impurities that are not detectable in RP-HPLC analysis are readily separated and detected. With the advent of capillary array electrophoresis (CAE), which allows for automated, parallel analysis of many different samples, we believe that FSCE will be especially applicable to the analysis of combinatorial synthesis products, by allowing researchers to evaluate many different samples in a single, highly parallel, fully automated analysis. This is in contrast to RP-HPLC analysis, in which samples must be analyzed in series.
View details for DOI 10.1021/bc0155871
View details for Web of Science ID 000175684800036
View details for PubMedID 12009959
Comb-like copolymers as self-coating, low-viscosity and high-resolution matrices for DNA sequencing
2002; 23 (10): 1441-1449
Comb-like copolymers with a polyacrylamide backbone and poly(N,N-dimethylacrylamide) grafts were prepared, as a way to combine the superior sieving properties of polyacrylamide with the self-coating properties of polydimethylacrylamide. These matrices function well in the absence of a capillary coating, and achieve separation performances for single-stranded DNA that are comparable to those of state-of-the-art long-chain linear polyacrylamide. Structural parameters such as the grafting density and the polymer molecular mass were varied, and good performance appears to be achieved with a relatively large range of parameters. Surprisingly, excellent separation is achieved even with matrices that have a viscosity as low as 200 mPa/s. A discussion of the physics underlying this behavior is provided.
View details for Web of Science ID 000175992800010
View details for PubMedID 12116154
Functional materials for microscale genomic and proteomic analyses
CURRENT OPINION IN BIOTECHNOLOGY
2002; 13 (2): 87-94
The design of functional materials for genomic and proteomic analyses in microscale systems has begun to mature, from materials designed for capillary-based electrophoresis systems to those tailored for microfluidic-based or 'chip-based' platforms. In particular, recent research has focused on evaluating different polymer chemistries for microchannel surface passivation and improved DNA separation matrix performance. Additionally, novel bioconjugate materials designed specifically for electrophoretic separations in microscale channels are facilitating new separation modalities.
View details for Web of Science ID 000174643900002
View details for PubMedID 11950557
Extreme stability of helices formed by water-soluble poly-N-substituted glycines (polypeptoids) with alpha-chiral side chains
2002; 63 (1): 12-20
Poly-N-substituted glycines or "peptoids" are protease-stable peptide mimics. Although the peptoid backbone is achiral and lacks hydrogen-bond donors, substitution with alpha-chiral side chains can drive the formation of stable helices that give rise to intense CD spectra. To systematically study the solution properties and stability of water-soluble peptoid helices with alpha-chiral side chains, we have synthesized and characterized an amphipathic, 36-residue N-substituted glycine oligomer. CD was used to investigate effects of concentration and solvent environment on this helical peptoid. We saw no significant dependence of helical structure on concentration. Intense, "alpha-helix-like" CD spectra were observed for the 36-mer in aqueous, 2,2,2-trifluorethanol (TFE), and methanol solution, proving a relative insensitivity of peptoid helical structure to solvent environment. While CD spectra taken in these different solvents were fundamentally similar in shape, we did observe some interesting differences in the intensities of particular CD bands in the various solvents. For example, the addition of TFE to an aqueous solvent increases the degree of peptoid helicity, as is observed for polypeptide alpha-helices. Moreover, the helical structure of peptoids appears to be virtually unaffected by heat, even in an aqueous buffer containing 8 M urea. The extraordinary resistance of these peptoid helices to denaturation is consistent with a dominant role of steric forces in their structural stabilization. The structured polypeptoids studied here may have potential as robust mimics of helical polypeptides of therapeutic interest.
View details for Web of Science ID 000173078300002
View details for PubMedID 11754344
The use of light scattering for precise characterization of polymers for DNA sequencing by capillary electrophoresis
2001; 22 (19): 4118-4128
The ability of a polymer matrix to separate DNA by capillary electrophoresis (CE) is strongly dependent upon polymer physical properties. In particular, recent results have shown that DNA sequencing performance is very sensitive to both the average molar mass and the average coil radius of the separation matrix polymers, which are affected by both polymer structure and polymer-solvent affinity. Large polymers with high average molar mass provide the best DNA sequencing separations for CE, but are also the most challenging to characterize with accuracy. The methods most commonly used for the characterization of water-soluble polymers with application in microchannel electrophoresis have been gel permeation chromatography (GPC) and intrinsic viscosity measurements, but the limitations and potential inaccuracies of these approaches, particularly for large or novel polymers and copolymers, press the need for a more universally accurate method of polymer molar mass profiling for advanced DNA separation matrices. Here, we show that multi-angle laser light scattering (MALLS) measurements, carried out either alone or in tandem with prior on-line sample fractionation by GPC, can provide accurate molar mass and coil radius information for polymer samples that are useful for DNA sequencing by CE. Wider employment of MALLS for characterization of novel polymers designed as DNA separation matrices for microchannel electrophoresis should enable more rapid optimization of matrix properties and formulation, and assist in the development of novel classes of polymer matrices.
View details for Web of Science ID 000172758100006
View details for PubMedID 11824632
Capillary electrophoretic separation of uncharged polymers using polyelectrolyte engines - Theoretical model
14th International Symposium on Microscale Separations and Analysis
ELSEVIER SCIENCE BV. 2001: 43–52
We recently demonstrated that the molecular mass distribution of an uncharged polymer sample can be analyzed using free-solution capillary electrophoresis of DNA-polymer conjugates. In these conjugates, the DNA is providing the electromotive force while the uncharged polydisperse polymer chains of the sample retard the DNA engine with different amounts of hydrodynamic drag. Here we present a theoretical model of this new analytical method. We show that for the most favourable, diffusion-limited electrophoresis conditions, there is actually an optimal DNA size to achieve the separation of a given polymer sample. Moreover, we demonstrate that the effective friction coefficient of the polymer chains is related to the stiffness of the two polymers of the conjugate, thus offering a method to estimate the persistence length of the uncharged polymer through mobility measurements. Finally, we compare some of our predictions with available experimental results.
View details for Web of Science ID 000170359200004
View details for PubMedID 11521894
Peptoid oligomers with alpha-chiral, aromatic side chains: Sequence requirements for the formation of stable peptoid helices
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2001; 123 (28): 6778-6784
The achiral backbone of oligo-N-substituted glycines or "peptoids" lacks hydrogen-bond donors, effectively preventing formation of the regular, intrachain hydrogen bonds that stabilize peptide alpha-helical structures. Yet, when peptoids are N-substituted with alpha-chiral, aromatic side chains, oligomers with as few as five residues form stable, chiral, polyproline-like helices in either organic or aqueous solution. The adoption of chiral secondary structure in peptoid oligomers is primarily driven by the steric influence of these bulky, chiral side chains. Interestingly, peptoid helices of this class exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have taken advantage of this distinctive spectroscopic signature to investigate sequence-related factors that favor and disfavor stable formation of peptoid helices of this class, through a comparison of more than 30 different heterooligomers with mixed chiral and achiral side chains. For this family of peptoids, we observe that a composition of at least 50% alpha-chiral, aromatic residues is necessary for the formation of stable helical structure in hexameric sequences. Moreover, both CD and 1H-13C HSQC NMR studies reveal that these short peptoid helices are stabilized by the placement of an alpha-chiral, aromatic residue on the carboxy terminus. Additional stabilization can be provided by the presence of an "aromatic face" on the helix, which can be patterned by positioning aromatic residues with three-fold periodicity in the sequence. Extending heterooligomer chain length beyond 12-15 residues minimizes the impact of the placement, but not the percentage, of alpha-chiral aromatic side chains on overall helical stability. In light of these new data, we discuss implications for the design of helical, biomimetic peptoids based on this structural motif.
View details for DOI 10.1021/ja003154n
View details for Web of Science ID 000169803000005
View details for PubMedID 11448181
Molar mass profiling of synthetic polymers by free-solution capillary electrophoresis of DNA-polymer conjugates
2001; 73 (8): 1795-1803
The molar mass distribution of a polymer sample is a critical determinant of its material properties and is generally analyzed by gel permeation chromatography or more recently, by MALDI-TOF mass spectrometry. We describe here a novel method for the determination of the degree of polymerization of polydisperse, uncharged, water-soluble polymers (e.g., poly(ethylene glycol) (PEG)), based upon single-monomer resolution of DNA-polymer conjugates by free-solution capillary electrophoresis. This is accomplished by end-on covalent conjugation of a polydisperse, uncharged polymer sample (PEG) to a monodisperse, fluorescently labeled DNA oligomer, followed by electrophoretic analysis. The monodisperse, charged DNA "engine" confers to each conjugate an equal amount of electromotive force, while the varying contour lengths of the uncharged, polydisperse polymers engender different amounts of hydrodynamic drag. The balance of electromotive and hydrodynamic forces enables rapid, high-resolution separation of the DNA-polymer conjugates as a function of the size of the uncharged PEG tail. This provides a profile of the molar mass distribution of the original polymer sample that can be detected by laser-induced fluorescence through excitation of the dye-labeled DNA. We call this method free solution conjugate electrophoresis (FSCE). Theory-based analysis of the resulting electrophoresis data allows precise calculation of the degree of polymerization of the PEG portion of each conjugate molecule. Knowledge of the molecular mass of the uncharged polymer's repeat unit allows for direct calculation of the molar mass averages as well as sample polydispersity index. The results of these analyses are strikingly reminiscent of MALDI-TOF spectra taken of the same PEG samples. PEG samples of 3.4-, 5-, and 20-kDa nominal average molar mass were analyzed by FSCE and MALDI-TOF; the values of the molar mass averages, Mw and Mn, typically agree to within 5%. Measurements and molar mass calculations are performed without any internal standards or calibration. Moreover, when DNA-polymer conjugate analysis is performed in a chip-based electrophoresis system, separation is complete in less than 13 min. FSCE offers an alternative to MALDI-TOF for the characterization of uncharged, water-soluble polymers that can be uniquely conjugated to DNA.
View details for Web of Science ID 000168156600019
View details for PubMedID 11338593
Peptoid oligomers with alpha-chiral, aromatic side chains: Effects of chain length on secondary structure
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2001; 123 (13): 2958-2963
Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.
View details for DOI 10.1021/ja003153v
View details for Web of Science ID 000167806300003
View details for PubMedID 11457005
Impact of polymer hydrophobicity on the properties and performance of DNA sequencing matrices for capillary electrophoresis
2001; 22 (4): 737-747
To elucidate the impact of matrix chemical and physical properties on DNA sequencing separations by capillary electrophoresis (CE), we have synthesized, characterized and tested a controlled set of different polymer formulations for this application. Homopolymers of acrylamide and N,N-dimethylacrylamide (DMA) and copolymers of DMA and N,N-diethylacrylamide (DEA) were synthesized by free radical polymerization and purified. Polymer molar mass distributions were characterized by tandem gel permeation chromatography - laser light scattering. Polymers with different chemical compositions and similar molar mass distributions were selected and employed at the same concentration so that the variables of comparison between them were hydrophobicity and average coil size in aqueous solution. We find that the low-shear viscosities of 7% w/v polymer solutions decrease by orders of magnitude with increasing polymer hydrophobicity, while hydrophilic polymers exhibit more pronounced reductions in viscosity with increased shear. The performance of the different matrices for DNA sequencing was compared with the same sample under identical CE conditions. The longest read length was produced with linear polyacrylamide (LPA) while linear poly-N,N-dimethylacrylamide (PDMA) gave approximately 100 fewer readable bases. Read lengths with DMA/DEA copolymers were lower, and decreased with increasing DEA content. This study highlights the importance of polymer hydrophilicity for high-performance DNA sequencing matrices, through the formation of robust, highly-entangled polymer networks and the minimization of hydrophobic interactions between polymers and fluorescently-labeled DNA molecules. However, the results also show that more hydrophobic matrices offer much lower viscosities, enabling easier microchannel loading at low applied pressures.
View details for Web of Science ID 000167424700016
View details for PubMedID 11296929
Microchannel DNA sequencing matrices with a thermally controlled "viscosity switch"
2001; 73 (2): 157-164
Polymers and hydrogels that swell or shrink in response to environmental stimuli such as changes in temperature, pH, or ionic strength are of interest as switchable materials for applications in biotechnology. In this paper, we show that thermoresponsive polymers offer some particular advantages as entangled matrices for DNA sequencing by capillary and microchip electrophoresis. Matrices based on conventional water-soluble polymers demand a compromise in their design for microchannel electrophoresis: whereas highly entangled solutions of high molar mass polymers provide optimal sequencing performance, their highly viscous solutions require application of high pressures to be loaded into electrophoresis microchannels. Here, we demonstrate the reproducible synthesis, precise characterization, and excellent DNA sequencing performance of high molar mass, thermoresponsive polymer matrices that exhibit a reversible, temperature-controlled "viscosity switch" from high-viscosity solutions at 25 degrees C to low-viscosity, microphase-separated colloidal dispersions at a chosen, elevated temperature. The viscosity switch decouples matrix loading and sieving properties, enabling acceleration of microchannel flow by 3 orders of magnitude. DNA sequencing separations yielding read lengths of 463 bases of contiguous sequence in 78 min with 97% base-calling accuracy can be achieved in these matrices. Switchable matrices will be particularly applicable to microfluidic devices with dynamic temperature control, which are likely to provide the next major leap in the efficiency of high-throughput DNA analysis.
View details for DOI 10.1021/ac001023z
View details for Web of Science ID 000166366000003
View details for PubMedID 11199960
Polymeric matrices for DNA sequencing by capillary electrophoresis
2000; 21 (18): 4096-4111
We review the wide range of polymeric materials that have been employed for DNA sequencing separations by capillary electrophoresis. Intensive research in the area has converged in showing that highly entangled solutions of hydrophilic, high molar mass polymers are required to achieve high DNA separation efficiency and long read length, system attributes that are particularly important for genomic sequencing. The extent of DNA-polymer interactions, as well as the robustness of the entangled polymer network, greatly influence the performance of a given polymer matrix for DNA separation. Further fundamental research in the field of polymer physics and chemistry is needed to elucidate the specific mechanisms by which DNA is separated in dynamic, uncross-linked polymer networks.
View details for Web of Science ID 000166102700015
View details for PubMedID 11192126
DNA sequencing up to 1300 bases in two hours by capillary electrophoresis with mixed replaceable linear polyacrylamide solutions
2000; 72 (5): 1045-1052
This paper presents results on ultralong read DNA sequencing with relatively short separation times using capillary electrophoresis with replaceable polymer matrixes. In previous work, the effectiveness of mixed replaceable solutions of linear polyacrylamide (LPA) was demonstrated, and 1000 bases were routinely obtained in less than 1 h. Substantially longer read lengths have now been achieved by a combination of improved formulation of LPA mixtures, optimization of temperature and electric field, adjustment of the sequencing reaction, and refinement of the base-caller. The average molar masses of LPA used as DNA separation matrixes were measured by gel permeation chromatography and multiangle laser light scattering. Newly formulated matrixes comprising 0.5% (w/w) 270 kDa and 2% (w/w) 10 or 17 MDa LPA raised the optimum column temperature from 60 to 70 degrees C, increasing the selectivity for large DNA fragments, while maintaining high selectivity for small fragments as well. This improved resolution was further enhanced by reducing the electric field strength from 200 to 125 V/cm. In addition, because sequencing accuracy beyond 1000 bases was diminished by the low signal from G-terminated fragments when the standard reaction protocol for a commercial dye primer kit was used, the amount of these fragments was doubled. Augmenting the base-calling expert system with rules specific for low peak resolution also had a significant effect, contributing slightly less than half of the total increase in read length. With full optimization, this read length reached up to 1300 bases (average 1250) with 98.5% accuracy in 2 h for a single-stranded M13 template.
View details for Web of Science ID 000085605100042
View details for PubMedID 10739210
Bioinspired polymeric materials: in-between proteins and plastics
CURRENT OPINION IN CHEMICAL BIOLOGY
1999; 3 (6): 681-687
Chemical and biological researchers are making rapid progress in the design and synthesis of non-natural oligomers and polymers that emulate the properties of natural proteins. Whereas molecular biologists are exploring biosynthetic routes to non-natural proteins with controlled material properties, synthetic polymer chemists are developing bioinspired materials with well-defined chemical and physical properties that function or self-organize according to defined molecular architectures. Bioorganic chemists, on the other hand, are developing several new classes of non-natural oligomers that are bridging the gap between molecular biology and polymer chemistry. These synthetic oligomers have both sidechain and length specificity, and, in some cases, demonstrate capability for folding, self-assembly, and specific biorecognition. Continued active exploration of diverse backbone and sidechain chemistries and connectivities in bioinspired oligomers will offer the potential for self-organized materials with greater chemical diversity and biostability than natural peptides. Taken together, advances in molecular bioengineering, polymer chemistry, and bioorganic chemistry are converging towards the creation of useful bioinspired materials with defined molecular properties.
View details for Web of Science ID 000084123300007
View details for PubMedID 10600724
Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
1998; 95 (8): 4303-4308
We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide alpha-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the alpha-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.
View details for Web of Science ID 000073120800044
View details for PubMedID 9539732
NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
1998; 95 (8): 4309-4314
Polymers of N-substituted glycines ("peptoids") containing chiral centers at the alpha position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of approximately 6 A. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.
View details for Web of Science ID 000073120800045
View details for PubMedID 9539733
Capillary electrophoresis of DNA in uncrosslinked polymer solutions: Evidence for a new mechanism of DNA separation
Biochemical Engineering IX - Interdisciplinary Foundations for Creating New Biotechnology
JOHN WILEY & SONS INC. 1996: 259–70
The electrophoretic separation of DNA molecules is usually performed in thin slabs of agarose or polyacrylamide gel. However, DNA separations can be achieved more rapidly and efficiently within a microbore fused silica capillary filled with an uncrosslinked polymer solution. An early assumption was that the mechanism of DNA separation in polymer solution-capillary electrophoresis (PS-CE) is the same as that postulated to occur in slab gel electrophoresis, i.e., that entangled polymer chains form a network of "pores" through which the DNA migrates. However, we have demonstrated that large DNA restriction fragments (2.0-23.1 kbp) can be separated by CE in extremely dilute polymer solutions, which contain as little as 6 parts per million [0.0006% (w/w)] of uncrosslinked hydroxyethyl cellulose (HEC) polymers. In such extremely dilute HEC solutions, far below the measured polymer entanglement threshold concentration, pore-based models of DNA electrophoresis do not apply. We propose a transient entanglement coupling mechanism for the electrophoretic separation of DNA in uncrosslinked polymer solutions, which is based on physical polymer/DNA interactions.
View details for Web of Science ID A1996VH45000008
View details for PubMedID 18629893
Electrophoresis of DNA in novel thermoreversible matrices
1996; 17 (9): 1460-1469
We demonstrate the feasibility of temperature-sensitive polymers as novel matrices for capillary and slab electrophoresis of DNA. These matrices combine the case-of-use of agarose with resolution properties of polyacrylamide. Two classes of matrices are used: (i) aqueous suspensions of gel microspheres and (ii) solutions containing uncross-linked temperature-sensitive polymers. When heated, the viscosity of these solutions drops dramatically because of the phase transition behavior of these polymers, and therefore these formulations are easy to pour or load. Results are presented for separation of double-stranded DNA fragments (< 2000 bp) in capillary, tube, and slab electrophoresis. Preliminary results are also presented for separation of single-stranded sequencing fragments by capillary electrophoresis. In the tube format, good resolution was obtained for phi X174/HaeIII fragments. In the slab format, excellent resolution of double-stranded DNA was obtained, including simultaneous separation of a 10 bp ladder up to 150 base pairs. In the capillary format, pBR322/MspI fragments were completely resolved, and single-base resolution of sequencing fragments was obtained up to 150 bases. We believe that temperature-sensitive polymers represent a new and promising class of electrophoretic media.
View details for Web of Science ID A1996VP14000009
View details for PubMedID 8905262
Capillary electrophoretic separation of DNA restriction fragments in mixtures of low- and high-molecular-weight hydroxyethylcellulose
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
1996; 35 (9): 2900-2908
View details for Web of Science ID A1996VF78500011
The effects of polymer properties on DNA separations by capillary electrophoresis in uncross-linked polymer solutions
1996; 17 (4): 744-757
Low-viscosity, aqueous solutions of hydrophilic linear polymers have been shown to be useful for the separation of DNA restriction fragments by capillary electrophoresis (CE). However, the choice of polymer type, size, and concentration remains largely empirical, because the mechanism of high-field electrophoretic DNA separations in polymer solutions is not well understood. To assist in elucidating the mechanism of DNA separation, we experimentally investigated the effects of polymer properties such as stiffness (persistence length), average molecular mass, polydispersity, and hydrophilicity on the separation of DNA ranging from 72 bp to 23 kbp. This was accomplished by comparing the results of DNA separations obtained by counter-migration CE in dilute and semidilute solutions of linear polyacrylamide (PAA), hydroxyethyl-cellulose (HEC), and hydroxypropylcellulose (HPC) polymers of several different average molecular masses.
View details for Web of Science ID A1996UP01600020
View details for PubMedID 8738338
THE USE OF COATED AND UNCOATED CAPILLARIES FOR THE ELECTROPHORETIC SEPARATION OF DNA IN DILUTE POLYMER-SOLUTIONS
1995; 16 (1): 64-74
We show that both uncoated and polyacrylamide-coated capillaries provide separation of large DNA restriction fragments (2.0-23.1 kbp) by capillary electrophoresis in dilute cellulosic polymer solutions. Uncoated capillaries, however, provide significantly better resolution of DNA fragments, particularly when ultra-dilute polymer solutions are used. This is because electroosmotic flow in uncoated capillaries increases the residence time of DNA in the capillary, without significantly contributing to band-broadening. At a given field strength and polymer concentration in the buffer, the electrophoretic mobilities of DNA restriction fragments in coated capillaries are virtually identical to those previously measured in uncoated capillaries. It is concluded that the fused silica surface of the capillary does not play a significant role in the mechanism of DNA separation by capillary electrophoresis in uncrosslinked polymer solutions. Thus, the separation of large DNA which has been observed to occur in ultra-dilute polymer solutions arises primarily from entanglement interactions between the cellulosic polymers and DNA restriction fragments which occur within the bulk of the polymer solution.
View details for Web of Science ID A1995QG96500012
View details for PubMedID 7737093
DNA SEPARATIONS BY SLAB GEL AND CAPILLARY ELECTROPHORESIS - THEORY AND PRACTICE
SEPARATION AND PURIFICATION METHODS
1995; 24 (1): 1-118
View details for Web of Science ID A1995RD20300001
A TRANSIENT ENTANGLEMENT COUPLING MECHANISM FOR DNA SEPARATION BY CAPILLARY ELECTROPHORESIS IN ULTRADILUTE POLYMER-SOLUTIONS
1994; 15 (5): 597-615
Using capillary electrophoresis, large DNA molecules (2.0-23.1 kbp) may be rapidly separated in ultradilute polymer solutions (< 0.002% w/w) under a high-voltage, steady field (265 V/cm). At this polymer concentration, the separation mechanism appears to be significantly different from that postulated to occur in crosslinked gels. Based on experimental results obtained with DNA restriction fragments and with negatively charged latex microspheres, we conclude that the Ogston and reptation models typically used to describe gel electrophoresis are not appropriate for DNA separations in such dilute polymer solutions. Electrophoresis experiments employing solutions of both small and large hydroxyethyl cellulose polymers highlight the importance of polymer length and concentration for the optimum resolution of DNA fragments varying in size from 72 bp to 23.1 kbp. A transient entanglement coupling mechanism for DNA separation in dilute polymer solutions is developed, which suggests that there is no a priori upper size limit to DNA that can be separated by capillary electrophoresis in a constant field.
View details for Web of Science ID A1994NU19900010
View details for PubMedID 7925237
CAPILLARY ELECTROPHORESIS OF DNA IN UNCROSS-LINKED POLYMER-SOLUTIONS
5th International Symposium on High Performance Capillary Electrophoresis (HPCE 93)
ELSEVIER SCIENCE BV. 1993: 3–16
We have used dilute and semi-dilute uncross-linked hydroxyethyl cellulose (HEC) solutions as separation matrices for capillary electrophoresis of DNA restriction fragments. In these experiments, we investigated the effects of HEC molecular weight and concentration on resolution, attempting to relate these parameters to the polymer entanglement threshold concentration. The entanglement thresholds of seven molecular weight fractions of hydroxyethyl cellulose were determined from viscosity-concentration data; the entanglement threshold was found to scale as N-1.2, where N = number of HEC monomers. This finding is not in agreement with classical scaling arguments. We present a relationship to predict the observed entanglement threshold of HEC in solution as a function of number average molecular weight. It was found that excellent separation of phi X174/HaeIII DNA restriction fragments (72-1353 base pairs) by capillary electrophoresis in HEC solutions can be achieved significantly below the entanglement threshold, depending on DNA size and HEC molecular weight. The mechanism of separation in these uncross-linked polymer solutions must therefore be reexamined. Our experiments show that the entanglement threshold is a useful parameter in predicting a range of HEC concentrations which will separate certain DNA fragments for a given HEC molecular weight. However, the presence of a fully entangled network is not a prerequisite for separation.
View details for Web of Science ID A1993MW21900002
View details for PubMedID 8281261