Honors & Awards
NSERC PDF, (Canada) (2018-2020)
Philips Healthcare Fellow, Philips, Stanford (2018-2019)
Dean's Fellowship (School of Medicine), Stanford (2017-2018)
Carl A. Winkler award for outstanding academic excellence – Thesis award, McGill University (2016-2017)
Sterry Hunt award for outstanding services as a Teaching assistant, McGill University (Chemistry departement) (2012/1 - 2013/9)
Nicolas Jaber Prize for academic excellence ( top 10 in the faculty of arts and science), American University of Beirut (AUB) (June 2009)
Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions
2015; 9 (12): 11898-11908
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
View details for DOI 10.1021/acsnano.5b04387
View details for Web of Science ID 000367280100038
View details for PubMedID 26556531
Stepwise growth of surface-grafted DNA nanotubes visualized at the single-molecule level
2015; 7 (4): 295-300
DNA nanotubes offer a high aspect ratio and rigidity, attractive attributes for the controlled assembly of hierarchically complex linear arrays. It is highly desirable to control the positioning of rungs along the backbone of the nanotubes, minimize the polydispersity in their manufacture and reduce the building costs. We report here a solid-phase synthesis methodology in which, through a cyclic scheme starting from a 'foundation rung' specifically bound to the surface, distinct rungs can be incorporated in a predetermined manner. Each rung is orthogonally addressable. Using fluorescently tagged rungs, single-molecule fluorescence studies demonstrated the robustness and structural fidelity of the constructs and confirmed the incorporation of the rungs in quantitative yield (>95%) at each step of the cycle. Prototype structures that consisted of up to 20 repeat units, about 450 nm in contour length, were constructed. Combined, the solid-phase synthesis strategy described and its visualization through single-molecule spectroscopy show good promise for the production of custom-made DNA nanotubes.
View details for DOI 10.1038/NCHEM.2184
View details for Web of Science ID 000351756200008
View details for PubMedID 25803467
Interaction of Anionic Phenylene Ethynylene Polymers with Lipids: From Membrane Embedding to Liposome Fusion
2014; 30 (35): 10704-10711
Here we report spectroscopic studies on the interaction of negatively charged, amphiphilic polyphenylene ethynylene (PPE) polymers with liposomes prepared either from negative, positive or zwitterionic lipids. Emission spectra of PPEs of 7 and 49 average repeat units bearing carboxylate terminated side chains showed that the polymer embeds within positively charged lipids where it exists as free chains. No interaction was observed between PPEs and negatively charged lipids. Here the polymer remained aggregated giving rise to broad emission spectra characteristic of the aggregate species. In zwitterionic lipids, we observed that the majority of the polymer remained aggregated yet a small fraction readily embedded within the membrane. Titration experiments revealed that saturation of zwitterionic lipids with polymer typically occurred at a polymer repeat unit to lipid mole ratio close to 0.05. No further membrane embedding was observed above that point. For liposomes prepared from positively charged lipids, saturation was observed at a PPE repeat unit to lipid mole ratio of ∼0.1 and liposome precipitation was observed above this point. FRET studies showed that precipitation was preceded by lipid mixing and liposome fusion induced by the PPEs. This behavior was prominent for the longer polymer and negligible for the shorter polymer at a repeat unit to lipid mole ratio of 0.05. We postulate that fusion is the consequence of membrane destabilization whereby the longer polymer gives rise to more extensive membrane deformation than the shorter polymer.
View details for DOI 10.1021/la502572u
View details for Web of Science ID 000341543100019
View details for PubMedID 25115171
Simple Design for DNA Nanotubes from a Minimal Set of Unmodified Strands: Rapid, Room-Temperature Assembly and Readily Tunable Structure
2013; 7 (4): 3022-3028
DNA nanotubes have great potential as nanoscale scaffolds for the organization of materials and the templation of nanowires and as drug delivery vehicles. Current methods for making DNA nanotubes either rely on a tile-based step-growth polymerization mechanism or use a large number of component strands and long annealing times. Step-growth polymerization gives little control over length, is sensitive to stoichiometry, and is slow to generate long products. Here, we present a design strategy for DNA nanotubes that uses an alternative, more controlled growth mechanism, while using just five unmodified component strands and a long enzymatically produced backbone. These tubes form rapidly at room temperature and have numerous, orthogonal sites available for the programmable incorporation of arrays of cargo along their length. As a proof-of-concept, cyanine dyes were organized into two distinct patterns by inclusion into these DNA nanotubes.
View details for DOI 10.1021/nn4006329
View details for Web of Science ID 000318143300015
View details for PubMedID 23452006
Improved immunoassay sensitivity and specificity using single-molecule colocalization.
2022; 13 (1): 5359
Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-alpha, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.
View details for DOI 10.1038/s41467-022-32796-x
View details for PubMedID 36097164
Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems.
Advanced materials (Deerfield Beach, Fla.)
Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.
View details for DOI 10.1002/adma.202003704
View details for PubMedID 33165999
Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques
ACCOUNTS OF CHEMICAL RESEARCH
2019; 52 (11): 3199–3210
DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.
View details for DOI 10.1021/acs.accounts.9b00424
View details for Web of Science ID 000498287700020
View details for PubMedID 31675207
Independent control of the thermodynamic and kinetic properties of aptamer switches.
2019; 10 (1): 5079
Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications.
View details for DOI 10.1038/s41467-019-13137-x
View details for PubMedID 31699984
Kinetics of Strand Displacement and Hybridization on Wireframe DNA Nanostructures: Dissecting the Roles of Size, Morphology, and Rigidity
2018; 12 (12): 12836–46
Dynamic wireframe DNA structures have gained significant attention in recent years, with research aimed towards using these architectures for sensing and encapsulation applications. For these assemblies to reach their full potential, however, knowledge on the rates of strand displacement and hybridization on these constructs is required. Herein, we report the use of single molecule fluorescence methodologies to observe the reversible switching between double- and single-stranded forms of triangular wireframe DNA nanotubes. Specifically, by using fluorescently labeled DNA strands, we were able to monitor changes in intensity over time as we introduced different sequences. This allowed us to extract detailed kinetic information on the strand displacement and hybridization processes. Due to the polymeric NT structure, the ability to individually address each of the three sides, and the inherent polydispersity of our samples as a result of the step polymerization by which they are formed, a library of compounds could be studied independently yet simultaneously. Kinetic models relying on simple exponential decays, multi-exponential decays or sigmoidal behavior were adjusted to the different constructs to retrieve erasing and refilling kinetics. Correlations were made between the kinetic behavior observed, the site accessibility, the nanotube length, and the structural robustness of wireframe DNA nanostructures, including fully single-stranded analogs. Overall, our results reveal how the length, morphology, and rigidity of the DNA framework modulate the kinetics of strand displacement and hybridization, as well as the overall addressability and structural stability of the structures under study.
View details for DOI 10.1021/acsnano.8b08016
View details for Web of Science ID 000454567500108
View details for PubMedID 30485067
Z-Profiling of CFTR Oligomerization State Distributions via Single Molecule Step Photobleaching Analysis in Epithelial Cells
59th Annual Meeting of the Biophysical-Society
CELL PRESS. 2015: 322A–322A
View details for Web of Science ID 000362849400030
Visualizing the Formation and Exploring the Structure and Dynamics of DNA-Architectures. A Single Molecule Study
57th Annual Meeting of the Biophysical-Society
CELL PRESS. 2013: 177A–177A
View details for Web of Science ID 000316074301403
Band, target, and onion patterns in Co(OH)(2) Liesegang systems
PHYSICAL REVIEW E
2011; 83 (1)
The study of morphology and shape development has gained considerable interest in certain sciences, notably biology and geology. Liesegang experiments producing Co(OH)2 stratification are performed here, in one, two, and three dimensions for comparison of the pattern morphologies. We obtain well-resolved bands in one dimension, target patterns (rings) in two dimensions, and onion patterns (spherical shells) in three dimensions. The morphological characteristics of the various patterns (spacing coefficients, rate of growth of ring spacing with distance) were measured. The spacing ratio of the strata in the different spatial dimensions was found to be anticorrelated with the surface-to-volume ratio of the gel domain. Some studies featuring the importance of morphology in Liesegang systems are briefly surveyed.
View details for DOI 10.1103/PhysRevE.83.016109
View details for Web of Science ID 000286763100001
View details for PubMedID 21405746