Rebecca Pinals

All Publications

• Protein Corona Selectivity on Carbon Nanotube Biosensors is Driven by Surface Coating and Chirality Protein Corona Selectivity on Carbon Nanotube Biosensors is Driven by Surface Coating and Chirality Pinals, R. L., Li, H., Ramirez, R., Pfammatter, S., Zimmermann, M., Perez Torres, D. J., Flavel, B. S., Vukovic, L., Herrmann, I. K., Nißler, R. 2026
• Engineered 3D immuno-glial-neurovascular human miBrain model. Proceedings of the National Academy of Sciences of the United States of America Stanton, A. E., Bubnys, A., Agbas, E., James, B., Park, D. S., Jiang, A., Pinals, R. L., Liu, L., Truong, N., Loon, A., Staab, C., Cerit, O., Wen, H. L., Mankus, D., Bisher, M. E., Lytton-Jean, A. K., Kellis, M., Blanchard, J. W., Langer, R., Tsai, L. H. 2025; 122 (42): e2511596122

  Abstract

  Patient-specific, human-based cellular models integrating a biomimetic blood-brain barrier, immune, and myelinated neuron components are critically needed to enable accelerated, translationally relevant discovery of neurological disease mechanisms and interventions. To construct a human cell-based model that includes these features and all six major brain cell types needed to mimic disease and dissect pathological mechanisms, we have constructed, characterized, and utilized a multicellular integrated brain (miBrain) immuno-glial-neurovascular model by engineering a brain-inspired 3D hydrogel and identifying conditions to coculture these six brain cell types, all differentiated from patient induced pluripotent stem cells. miBrains recapitulate in vivo-like hallmarks inclusive of neuronal activity, functional connectivity, barrier function, myelin-producing oligodendrocyte engagement with neurons, multicellular interactions, and transcriptomic profiles. We implemented the model to study Alzheimer's Disease pathologies associated with APOE4 genetic risk. APOE4 miBrains differentially exhibit amyloid aggregation, tau phosphorylation, and astrocytic glial fibrillary acidic protein. Unlike the coemergent fate specification of glia and neurons in other organoid approaches, miBrains integrate independently differentiated cell types, a feature we harnessed to identify that APOE4 in astrocytes promotes neuronal tau pathogenesis and dysregulation through crosstalk with microglia.

  View details for DOI 10.1073/pnas.2511596122

  View details for PubMedID 41105712

  View details for PubMedCentralID PMC12557797

• Protein corona formed on lipid nanoparticles compromises delivery efficiency of mRNA cargo. Nature communications Voke, E., Arral, M. L., Squire, H. J., Lin, T. J., Zheng, L., Coreas, R., Lui, A., Iavarone, A. T., Pinals, R. L., Whitehead, K. A., Landry, M. P. 2025; 16 (1): 8699

  Abstract

  Lipid nanoparticles (LNPs) are the most clinically advanced nonviral RNA-delivery vehicles, though challenges remain in fully understanding how LNPs interact with biological systems. In vivo, proteins form an associated corona on LNPs that redefines their physicochemical properties and influences delivery outcomes. Despite its importance, the LNP protein corona is challenging to study owing to the technical difficulty of selectively recovering soft nanoparticles from biological samples. Herein, we develop a quantitative, label-free mass spectrometry-based proteomics approach to characterize the protein corona on LNPs. Critically, this protein corona isolation workflow avoids artifacts introduced by the presence of endogenous nanoparticles in human biofluids. We apply continuous density gradient ultracentrifugation for protein-LNP complex isolation, with mass spectrometry for protein identification normalized to protein composition in the biofluid alone. With this approach, we quantify proteins consistently enriched in the LNP corona including vitronectin, C-reactive protein, and alpha-2-macroglobulin. We explore the impact of these corona proteins on cell uptake and mRNA expression in HepG2 human liver cells, and find that, surprisingly, increased levels of cell uptake do not correlate with increased mRNA expression in part due to protein corona-induced lysosomal trafficking of LNPs. Our results underscore the need to consider the protein corona in the design of LNP-based therapeutics.

  View details for DOI 10.1038/s41467-025-63726-2

  View details for PubMedID 41027853

  View details for PubMedCentralID 8386155

• Vascular-Perfusable Human 3D Brain-on-Chip. bioRxiv : the preprint server for biology Stanton, A. E., Pinals, R. L., Choi, A., Truong, N., Kang, E., Jiang, A., Lozano Cruz, C. F., Hawkins, S., Sarcar, R., Volkova, A., King, O., Agbas, E., Nakano, M., Chiu, C., Bubnys, A., Wright, S., Staab, C., Bikdash, R., Forden, E., Langer, R., Tsai, L. 2025

  Abstract

  Development and delivery of treatments for neurological diseases are limited by the tight and selective human blood-brain barrier (BBB). Although animal models have been important research and preclinical tools, the rodent BBB exhibits species differences and fails to capture the complexity of human genetics. Microphysiological systems incorporating human-derived cells hold great potential for modeling disease and therapeutic development, with advantages in screening throughput, real-time monitoring, and tunable genetic backgrounds when combined with induced pluripotent stem cell (iPSC) technology. Existing 3D BBB-on-chip systems have incorporated iPSC-derived endothelial cells but not the other major brain cell types from iPSCs, each of which contributes to brain physiology and disease. Here we developed a 3D Brain-Chip system incorporating endothelial cells, pericytes, astrocytes, neurons, microglia, and oligodendroglia from iPSCs. To enable this multicellular 3D co-culture in-chip, we designed a GelChip microfluidic platform using a 3D printing-based approach and dextran-based engineered hydrogel. Leveraging this platform, we co-cultured and characterized iPSC-derived brain-on-chips and modeled the brain microvasculature of APOE4 , the strongest known genetic risk factor for sporadic Alzheimer's disease. These 3D brain-on-chips provide a versatile system to assess BBB vascular morphology and function, investigate downstream neurological effects in disease, and screen therapeutics to optimize delivery to the brain.Significance Statement: The blood-brain barrier (BBB) is both a contributing factor to neurological disease and a major obstacle to its treatment, yet human-relevant models remain limited. Most existing brain-on-chip systems incorporate only subsets of BBB cell types and cannot capture the full cellular complexity of the human neurovascular unit. Here, we establish a vascular-perfusable 3D Brain-Chip using human induced pluripotent stem cell-derived brain cells including endothelial cells, pericytes, astrocytes, neurons, microglia, and oligodendroglia. This system enables systematic analysis of human genetic risk factors, such as APOE4 in Alzheimer's disease, and provides a powerful platform to investigate BBB function and dysfunction and accelerate the development of more effective neurological therapies.

  View details for DOI 10.1101/2025.09.18.676925

  View details for PubMedID 41000798

• Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry. Journal of the American Chemical Society Rosenberg, D. J., Cunningham, F. J., Hubbard, J. D., Goh, N. S., Wang, J. W., Nishitani, S., Hayman, E. B., Hura, G. L., Landry, M. P., Pinals, R. L. 2024; 146 (1): 386-398

  Abstract

  Single-walled carbon nanotubes (SWCNTs) with adsorbed single-stranded DNA (ssDNA) are applied as sensors to investigate biological systems, with potential applications ranging from clinical diagnostics to agricultural biotechnology. Unique ssDNA sequences render SWCNTs selectively responsive to target analytes such as (GT)n-SWCNTs recognizing the neuromodulator, dopamine. It remains unclear how the ssDNA conformation on the SWCNT surface contributes to functionality, as observations have been limited to computational models or experiments under dehydrated conditions that differ substantially from the aqueous biological environments in which the nanosensors are applied. We demonstrate a direct mode of measuring in-solution ssDNA geometries on SWCNTs via X-ray scattering interferometry (XSI), which leverages the interference pattern produced by AuNP tags conjugated to ssDNA on the SWCNT surface. We employ XSI to quantify distinct surface-adsorbed morphologies for two (GT)n ssDNA oligomer lengths (n = 6, 15) that are used on SWCNTs in the context of dopamine sensing and measure the ssDNA conformational changes as a function of ionic strength and during dopamine interaction. We show that the shorter oligomer, (GT)6, adopts a more periodically ordered ring structure along the SWCNT axis (inter-ssDNA distance of 8.6 ± 0.3 nm), compared to the longer (GT)15 oligomer (most probable 5'-to-5' distance of 14.3 ± 1.1 nm). During molecular recognition, XSI reveals that dopamine elicits simultaneous axial elongation and radial constriction of adsorbed ssDNA on the SWCNT surface. Our approach using XSI to probe solution-phase morphologies of polymer-functionalized SWCNTs can be applied to yield insights into sensing mechanisms and inform future design strategies for nanoparticle-based sensors.

  View details for DOI 10.1021/jacs.3c09549

  View details for PubMedID 38158616

  View details for PubMedCentralID PMC12285910

• Inferring local molecular dynamics from the global actin network structure: A case study of 2D synthetic branching actin networks. Journal of theoretical biology Rostami, M. W., Bannish, B. E., Gasior, K., Pinals, R. L., Copos, C., Dawes, A. T. 2023; 575: 111613

  Abstract

  Cells rely on their cytoskeleton for key processes including division and directed motility. Actin filaments are a primary constituent of the cytoskeleton. Although actin filaments can create a variety of network architectures linked to distinct cell functions, the microscale molecular interactions that give rise to these macroscale structures are not well understood. In this work, we investigate the microscale mechanisms that produce different branched actin network structures using an iterative classification approach. First, we employ a simple yet comprehensive agent-based model that produces synthetic actin networks with precise control over the microscale dynamics. Then we apply machine learning techniques to classify actin networks based on measurable network density and geometry, identifying key mechanistic processes that lead to particular branched actin network architectures. Extensive computational experiments reveal that the most accurate method uses a combination of supervised learning based on network density and unsupervised learning based on network symmetry. This framework can potentially serve as a powerful tool to discover the molecular interactions that produce the wide variety of actin network configurations associated with normal development as well as pathological conditions such as cancer.

  View details for DOI 10.1016/j.jtbi.2023.111613

  View details for PubMedID 37774939

  View details for PubMedCentralID PMC10842209

• Building in vitro models of the brain to understand the role of APOE in Alzheimer's disease. Life science alliance Pinals, R. L., Tsai, L. H. 2022; 5 (11)

  Abstract

  Alzheimer's disease (AD) is a devastating, complex, and incurable disease that represents an increasingly problematic global health issue. The etiology of sporadic AD that accounts for a vast majority of cases remains poorly understood, with no effective therapeutic interventions. Genetic studies have identified AD risk genes including the most prominent, APOE, of which the ɛ4 allele increases risk in a dose-dependent manner. A breakthrough discovery enabled the creation of human induced pluripotent stem cells (hiPSCs) that can be differentiated into various brain cell types, facilitating AD research in genetically human models. Herein, we provide a brief background on AD in the context of APOE susceptibility and feature work employing hiPSC-derived brain cell and tissue models to interrogate the contribution of APOE in driving AD pathology. Such models have delivered crucial insights into cellular mechanisms and cell type-specific roles underlying the perturbed biological functions that trigger pathogenic cascades and propagate neurodegeneration. Collectively, hiPSC-based models are envisioned to be an impactful platform for uncovering fundamental AD understanding, with high translational value toward AD drug discovery and testing.

  View details for DOI 10.26508/lsa.202201542

  View details for PubMedID 36167428

  View details for PubMedCentralID PMC9515460

• How Early-Career Scientists Responded with Resiliency to the Space Created by the COVID-19 Pandemic. ACS central science Fung, F. M., Jilani, S. Z., Ohnsorg, M. L., Pinals, R. L., Saraf, M., Tropp, J., Carlton, P. 2022; 8 (3): 294-296

  View details for DOI 10.1021/acscentsci.2c00094

  View details for PubMedID 35350605

  View details for PubMedCentralID PMC8949632

• Nanoparticle cellular internalization is not required for RNA delivery to mature plant leaves. Nature nanotechnology Zhang, H., Goh, N. S., Wang, J. W., Pinals, R. L., González-Grandío, E., Demirer, G. S., Butrus, S., Fakra, S. C., Del Rio Flores, A., Zhai, R., Zhao, B., Park, S. J., Landry, M. P. 2022; 17 (2): 197-205

  Abstract

  Rapidly growing interest in the nanoparticle-mediated delivery of DNA and RNA to plants requires a better understanding of how nanoparticles and their cargoes translocate in plant tissues and into plant cells. However, little is known about how the size and shape of nanoparticles influence transport in plants and the delivery efficiency of their cargoes, limiting the development of nanotechnology in plant systems. In this study we employed non-biolistically delivered DNA-modified gold nanoparticles (AuNPs) of various sizes (5-20 nm) and shapes (spheres and rods) to systematically investigate their transport following infiltration into Nicotiana benthamiana leaves. Generally, smaller AuNPs demonstrated more rapid, higher and longer-lasting levels of association with plant cell walls compared with larger AuNPs. We observed internalization of rod-shaped but not spherical AuNPs into plant cells, yet, surprisingly, 10 nm spherical AuNPs functionalized with small-interfering RNA (siRNA) were the most efficient at siRNA delivery and inducing gene silencing in mature plant leaves. These results indicate the importance of nanoparticle size in efficient biomolecule delivery and, counterintuitively, demonstrate that efficient cargo delivery is possible and potentially optimal in the absence of nanoparticle cellular internalization. Overall, our results highlight nanoparticle features of importance for transport within plant tissues, providing a mechanistic overview of how nanoparticles can be designed to achieve efficacious biocargo delivery for future developments in plant nanobiotechnology.

  View details for DOI 10.1038/s41565-021-01018-8

  View details for PubMedID 34811553

  View details for PubMedCentralID PMC10519342

• Supervised learning model predicts protein adsorption to carbon nanotubes. Science advances Ouassil, N., Pinals, R. L., Del Bonis-O'Donnell, J. T., Wang, J. W., Landry, M. P. 2022; 8 (1): eabm0898

  Abstract

  Engineered nanoparticles are advantageous for biotechnology applications including biomolecular sensing and delivery. However, testing compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable protein corona formation prevents their effective implementation. We develop a random forest classifier trained with mass spectrometry data to identify proteins that adsorb to nanoparticles based solely on the protein sequence (78% accuracy, 70% precision). We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)–based nanosensor and study the relationship between the protein’s amino acid–based properties and binding capacity. Protein features associated with increased likelihood of SWCNT binding include high content of solvent-exposed glycines and nonsecondary structure–associated amino acids. To evaluate its predictive power, we apply the classifier to identify proteins with high binding affinity to SWCNTs, with experimental validation. The developed classifier provides a step toward undertaking the otherwise intractable problem of predicting protein-nanoparticle interactions.

  View details for DOI 10.1126/sciadv.abm0898

  View details for PubMedID 34995109

  View details for PubMedCentralID PMC8741178

• In Planta Nanosensors: Understanding Biocorona Formation for Functional Design. ACS sensors Voke, E., Pinals, R. L., Goh, N. S., Landry, M. P. 2021; 6 (8): 2802-2814

  Abstract

  Climate change and population growth are straining agricultural output. To counter these changes and meet the growing demand for food and energy, the monitoring and engineering of crops are becoming increasingly necessary. Nanoparticle-based sensors have emerged in recent years as new tools to advance agricultural practices. As these nanoparticle-based sensors enter and travel through the complex biofluids within plants, biomolecules including proteins, metabolites, lipids, and carbohydrates adsorb onto the nanoparticle surfaces, forming a coating known as the "bio-corona". Understanding these nanoparticle-biomolecule interactions that govern nanosensor function in plants will be essential to successfully develop and translate nanoparticle-based sensors into broader agricultural practice.

  View details for DOI 10.1021/acssensors.1c01159

  View details for PubMedID 34279907

  View details for PubMedCentralID PMC10461777

• Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 Quantitative Reverse Transcription Polymerase Chain Reaction Detection Sensitivity. ACS nano Jeong, S., González-Grandío, E., Navarro, N., Pinals, R. L., Ledesma, F., Yang, D., Landry, M. P. 2021; 15 (6): 10309-10317

  Abstract

  The global SARS-CoV-2 coronavirus pandemic has led to a surging demand for rapid and efficient viral infection diagnostic tests, generating a supply shortage in diagnostic test consumables including nucleic acid extraction kits. Here, we develop a modular method for high-yield extraction of viral single-stranded nucleic acids by using "capture" ssDNA sequences attached to carbon nanotubes. Target SARS-CoV-2 viral RNA can be captured by ssDNA-nanotube constructs via hybridization and separated from the liquid phase in a single-tube system with minimal chemical reagents, for downstream quantitative reverse transcription polymerase chain reaction (RT-qPCR) detection. This nanotube-based extraction method enables 100% extraction yield of target SARS-CoV-2 RNA from phosphate-buffered saline in comparison to ∼20% extraction yield when using a commercial silica-column kit. Notably, carbon nanotubes enable extraction of nucleic acids directly from 50% human saliva with a similar efficiency as achieved with commercial DNA/RNA extraction kits, thereby bypassing the need for further biofluid purification and avoiding the use of commercial extraction kits. Carbon nanotube-based extraction of viral nucleic acids facilitates high-yield and high-sensitivity identification of viral nucleic acids such as the SARS-CoV-2 viral genome with a reduced reliance on reagents affected by supply chain obstacles.

  View details for DOI 10.1021/acsnano.1c02494

  View details for PubMedID 34105936

  View details for PubMedCentralID PMC8204751

• Rapid SARS-CoV-2 Spike Protein Detection by Carbon Nanotube-Based Near-Infrared Nanosensors. Nano letters Pinals, R. L., Ledesma, F., Yang, D., Navarro, N., Jeong, S., Pak, J. E., Kuo, L., Chuang, Y. C., Cheng, Y. W., Sun, H. Y., Landry, M. P. 2021; 21 (5): 2272-2280

  Abstract

  To effectively track and eliminate COVID-19, it is critical to develop tools for rapid and accessible diagnosis of actively infected individuals. Here, we introduce a single-walled carbon nanotube (SWCNT)-based optical sensing approach toward this end. We construct a nanosensor based on SWCNTs noncovalently functionalized with ACE2, a host protein with high binding affinity for the SARS-CoV-2 spike protein. The presence of the SARS-CoV-2 spike protein elicits a robust, 2-fold nanosensor fluorescence increase within 90 min of spike protein exposure. We characterize the nanosensor stability and sensing mechanism and passivate the nanosensor to preserve sensing response in saliva and viral transport medium. We further demonstrate that these ACE2-SWCNT nanosensors retain sensing capacity in a surface-immobilized format, exhibiting a 73% fluorescence turn-on response within 5 s of exposure to 35 mg/L SARS-CoV-2 virus-like particles. Our data demonstrate that ACE2-SWCNT nanosensors can be developed into an optical tool for rapid SARS-CoV-2 detection.

  View details for DOI 10.1021/acs.nanolett.1c00118

  View details for PubMedID 33635655

  View details for PubMedCentralID PMC10493163

• Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments. Angewandte Chemie (International ed. in English) Pinals, R. L., Yang, D., Rosenberg, D. J., Chaudhary, T., Crothers, A. R., Iavarone, A. T., Hammel, M., Landry, M. P. 2020; 59 (52): 23668-23677

  Abstract

  When nanoparticles enter biological environments, proteins adsorb to form the "protein corona" which alters nanoparticle biodistribution and toxicity. Herein, we measure protein corona formation on DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs), a nanoparticle used widely for sensing and delivery, in blood plasma and cerebrospinal fluid. We characterize corona composition by mass spectrometry, revealing high-abundance corona proteins involved in lipid binding, complement activation, and coagulation. We investigate roles of electrostatic and entropic interactions driving selective corona formation. Lastly, we study real-time protein binding on ssDNA-SWCNTs, obtaining agreement between enriched proteins binding strongly and depleted proteins binding marginally, while highlighting cooperative adsorption mechanisms. Knowledge of protein corona composition, formation mechanisms, and dynamics informs nanoparticle translation from in vitro design to in vivo application.

  View details for DOI 10.1002/anie.202008175

  View details for PubMedID 32931615

  View details for PubMedCentralID PMC7736064

• Mitigation of Carbon Nanotube Neurosensor Induced Transcriptomic and Morphological Changes in Mouse Microglia with Surface Passivation. ACS nano Yang, D., Yang, S. J., Del Bonis-O'Donnell, J. T., Pinals, R. L., Landry, M. P. 2020; 14 (10): 13794-13805

  Abstract

  Single-walled carbon nanotubes (SWCNT) are used in neuroscience for deep-brain imaging, neuron activity recording, measuring brain morphology, and imaging neuromodulation. However, the extent to which SWCNT-based probes impact brain tissue is not well understood. Here, we study the impact of (GT)6-SWCNT dopamine nanosensors on SIM-A9 mouse microglial cells and show SWCNT-induced morphological and transcriptomic changes in these brain immune cells. Next, we introduce a strategy to passivate (GT)6-SWCNT nanosensors with PEGylated phospholipids to improve both biocompatibility and dopamine imaging quality. We apply these passivated dopamine nanosensors to image electrically stimulated striatal dopamine release in acute mouse brain slices, and show that slices labeled with passivated nanosensors exhibit higher fluorescence response to dopamine and measure more putative dopamine release sites. Hence, this facile modification to SWCNT-based dopamine probes provides immediate improvements to both biocompatibility and dopamine imaging functionality with an approach that is readily translatable to other SWCNT-based neurotechnologies.

  View details for DOI 10.1021/acsnano.0c06154

  View details for PubMedID 32955853

  View details for PubMedCentralID PMC10539025

• Engineering at the nano-bio interface: harnessing the protein corona towards nanoparticle design and function. The Analyst Pinals, R. L., Chio, L., Ledesma, F., Landry, M. P. 2020; 145 (15): 5090-5112

  Abstract

  Unpredictable and uncontrollable protein adsorption on nanoparticles remains a considerable challenge to achieving effective application of nanotechnologies within biological environments. Nevertheless, engineered nanoparticles offer unprecedented functionality and control in probing and altering biological systems. In this review, we highlight recent advances in harnessing the "protein corona" formed on nanoparticles as a handle to tune functional properties of the protein-nanoparticle complex. Towards this end, we first review nanoparticle properties that influence protein adsorption and design strategies to facilitate selective corona formation, with the corresponding characterization techniques. We next focus on literature detailing corona-mediated functionalities, including stealth to avoid recognition and sequestration while in circulation, targeting of predetermined in vivo locations, and controlled activation once localized to the intended biological compartment. We conclude with a discussion of biocompatibility outcomes for these protein-nanoparticle complexes applied in vivo. While formation of the nanoparticle-corona complex may impede our control over its use for the projected nanobiotechnology application, it concurrently presents an opportunity to create improved protein-nanoparticle architectures by exploiting natural or guiding selective protein adsorption to the nanoparticle surface.

  View details for DOI 10.1039/d0an00633e

  View details for PubMedID 32608460

  View details for PubMedCentralID PMC7439532

• Binding Affinity and Conformational Preferences Influence Kinetic Stability of Short Oligonucleotides on Carbon Nanotubes ADVANCED MATERIALS INTERFACES Alizadehmojarad, A. A., Zhou, X., Beyene, A. G., Chacon, K. E., Sung, Y., Pinals, R. L., Landry, M. P., Vukovi, L. 2020; 7 (15)

  View details for DOI 10.1002/admi.202000353

  View details for Web of Science ID 000538608200001

• Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown. Science advances Demirer, G. S., Zhang, H., Goh, N. S., Pinals, R. L., Chang, R., Landry, M. P. 2020; 6 (26): eaaz0495

  Abstract

  Posttranscriptional gene silencing (PTGS) is a powerful tool to understand and control plant metabolic pathways, which is central to plant biotechnology. PTGS is commonly accomplished through delivery of small interfering RNA (siRNA) into cells. Standard plant siRNA delivery methods (Agrobacterium and viruses) involve coding siRNA into DNA vectors and are only tractable for certain plant species. Here, we develop a nanotube-based platform for direct delivery of siRNA and show high silencing efficiency in intact plant cells. We demonstrate that nanotubes successfully deliver siRNA and silence endogenous genes, owing to effective intracellular delivery and nanotube-induced protection of siRNA from nuclease degradation. This study establishes that nanotubes could enable a myriad of plant biotechnology applications that rely on RNA delivery to intact cells.

  View details for DOI 10.1126/sciadv.aaz0495

  View details for PubMedID 32637592

  View details for PubMedCentralID PMC7314522

• Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption. Scientific reports Jeong, S., Pinals, R. L., Dharmadhikari, B., Song, H., Kalluri, A., Debnath, D., Wu, Q., Ham, M. H., Patra, P., Landry, M. P. 2020; 10 (1): 7074

  Abstract

  Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.

  View details for DOI 10.1038/s41598-020-63769-z

  View details for PubMedID 32341425

  View details for PubMedCentralID PMC7184744

• Covalent Surface Modification Effects on Single-Walled Carbon Nanotubes for Targeted Sensing and Optical Imaging ADVANCED FUNCTIONAL MATERIALS Chio, L., Pinals, R. L., Murali, A., Goh, N. S., Landry, M. P. 2020; 30 (17)

  View details for DOI 10.1002/adfm.201910556

  View details for Web of Science ID 000530309100005

• Corona Exchange Dynamics on Carbon Nanotubes by Multiplexed Fluorescence Monitoring. Journal of the American Chemical Society Pinals, R. L., Yang, D., Lui, A., Cao, W., Landry, M. P. 2020; 142 (3): 1254-1264

  Abstract

  Noncovalent adsorption of DNA on nanoparticles has led to their widespread implementation as gene delivery tools and optical probes. Yet, the behavior and stability of DNA-nanoparticle complexes once applied in biomolecule-rich, in vivo environments remains unpredictable, whereby biocompatibility testing usually occurs in serum. Here, we demonstrate time-resolved measurements of exchange dynamics between solution-phase and adsorbed corona-phase DNA and protein biomolecules on single-walled carbon nanotubes (SWCNTs). We capture real-time binding of fluorophore-labeled biomolecules, utilizing the SWCNT surface as a fluorescence quencher, and apply this corona exchange assay to study protein corona dynamics on ssDNA-SWCNT-based dopamine sensors. We study exchange of two blood proteins, albumin and fibrinogen, adsorbing to and competitively displacing (GT)6 vs (GT)15 ssDNA from ssDNA-SWCNTs. We find that (GT)15 binds to SWCNTs with a higher affinity than (GT)6 and that fibrinogen interacts with ssDNA-SWCNTs more strongly than albumin. Albumin and fibrinogen cause a 52.2% and 78.2% attenuation of the dopamine nanosensor response, coinciding with 0.5% and 3.7% desorption of (GT)6, respectively. Concurrently, the total surface-adsorbed fibrinogen mass is 168% greater than that of albumin. Binding profiles are fit to a competitive surface exchange model which recapitulates the experimental observation that fibrinogen has a higher affinity for SWCNTs than albumin, with a fibrinogen on-rate constant 1.61-fold greater and an off-rate constant 0.563-fold smaller than that of albumin. Our methodology presents a generic route to assess real-time corona exchange on nanoparticles in solution phase and more broadly motivates testing of nanoparticle-based technologies in blood plasma rather than the more ubiquitously tested serum conditions.

  View details for DOI 10.1021/jacs.9b09617

  View details for PubMedID 31887029

  View details for PubMedCentralID PMC10493162

• Connecting Actin Polymer Dynamics Across Multiple Scales Using Mathematics to Understand Biological Complexity Copos, C., Bannish, B., Gasior, K., Pinals, R. L., Rostami, M. W., Dawes, A. T. Springer. 2020
• Chemometric Approaches for Developing Infrared Nanosensors To Image Anthracyclines. Biochemistry Del Bonis-O'Donnell, J. T., Pinals, R. L., Jeong, S., Thakrar, A., Wolfinger, R. D., Landry, M. P. 2019; 58 (1): 54-64

  Abstract

  Generation, identification, and validation of optical probes to image molecular targets in a biological milieu remain a challenge. Synthetic molecular recognition approaches leveraging the intrinsic near-infrared fluorescence of single-walled carbon nanotubes are promising for long-term biochemical imaging in tissues. However, generation of nanosensors for selective imaging of molecular targets requires a heuristic approach. Here, we present a chemometric platform for rapidly screening libraries of candidate single-walled carbon nanotube nanosensors against biochemical analytes to quantify the fluorescence response to small molecules, including vitamins, neurotransmitters, and chemotherapeutics. We further show this method can be applied to identify biochemical analytes that selectively modulate the intrinsic near-infrared fluorescence of candidate nanosensors. Chemometric analysis thus enables identification of nanosensor-analyte "hits" and also nanosensor fluorescence signaling modalities such as wavelength shifts that are optimal for translation to biological imaging. Through this approach, we identify and characterize a nanosensor for the chemotherapeutic anthracycline doxorubicin (DOX), which provides a ≤17 nm fluorescence red-shift and exhibits an 8 μM limit of detection, compatible with peak circulatory concentrations of doxorubicin common in therapeutic administration. We demonstrate the selectivity of this nanosensor over dacarbazine, a chemotherapeutic commonly co-injected with doxorubicin. Lastly, we establish nanosensor tissue compatibility for imaging of doxorubicin in muscle tissue by incorporating nanosensors into the mouse hindlimb and measuring the nanosensor response to exogenous DOX administration. Our results motivate chemometric approaches to nanosensor discovery for chronic imaging of drug partitioning into tissues and toward real-time monitoring of drug accumulation.

  View details for DOI 10.1021/acs.biochem.8b00926

  View details for PubMedID 30480442

  View details for PubMedCentralID PMC6411385

• Stochastic Simulation of Dopamine Neuromodulation for Implementation of Fluorescent Neurochemical Probes in the Striatal Extracellular Space. ACS chemical neuroscience Beyene, A. G., McFarlane, I. R., Pinals, R. L., Landry, M. P. 2017; 8 (10): 2275-2289

  Abstract

  Imaging the dynamic behavior of neuromodulatory neurotransmitters in the extracelluar space that arise from individual quantal release events would constitute a major advance in neurochemical imaging. Spatial and temporal resolution of these highly stochastic neuromodulatory events requires concurrent advances in the chemical development of optical nanosensors selective for neuromodulators in concert with advances in imaging methodologies to capture millisecond neurotransmitter release. Herein, we develop and implement a stochastic model to describe dopamine dynamics in the extracellular space (ECS) of the brain dorsal striatum to guide the design and implementation of fluorescent neurochemical probes that record neurotransmitter dynamics in the ECS. Our model is developed from first-principles and simulates release, diffusion, and reuptake of dopamine in a 3D simulation volume of striatal tissue. We find that in vivo imaging of neuromodulation requires simultaneous optimization of dopamine nanosensor reversibility and sensitivity: dopamine imaging in the striatum or nucleus accumbens requires nanosensors with an optimal dopamine dissociation constant (Kd) of 1 μM, whereas Kds above 10 μM are required for dopamine imaging in the prefrontal cortex. Furthermore, as a result of the probabilistic nature of dopamine terminal activity in the striatum, our model reveals that imaging frame rates of 20 Hz are optimal for recording temporally resolved dopamine release events. Our work provides a modeling platform to probe how complex neuromodulatory processes can be studied with fluorescent nanosensors and enables direct evaluation of nanosensor chemistry and imaging hardware parameters. Our stochastic model is generic for evaluating fluorescent neurotransmission probes, and is broadly applicable to the design of other neurotransmitter fluorophores and their optimization for implementation in vivo.

  View details for DOI 10.1021/acschemneuro.7b00193

  View details for PubMedID 28714693

  View details for PubMedCentralID PMC10494912

• Direct Conversion of Hydride- to Siloxane-Terminated Silicon Quantum Dots JOURNAL OF PHYSICAL CHEMISTRY C Anderson, R. T., Zang, X., Fernando, R., Dzara, M. J., Ngo, C., Sharps, M., Pinals, R., Pylypenko, S., Lusk, M. T., Sellinger, A. 2016; 120 (45): 25822-25831

  View details for DOI 10.1021/acs.jpcc.6b07930

  View details for Web of Science ID 000388429100019