Bernard Yurke

Programmable Periodicity of Quantum Dot Arrays with DNA Origami Nanotubes

To fabricate quantum dot arrays with programmable periodicity, functionalized DNA origami nanotubes were developed. Selected DNA staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of AFM images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.

Chiral plasmonic DNA nanostructures with switchable circular dichroism

Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed directional circular dichroism of our switchable plasmonic material is in good agreement with predictions based on dipole approximation theory. Such dynamic metamaterials introduce functionality into soft matter-based optical devices and may enable novel data storage schemes or signal modulators.

DNA-Controlled Excitonic Switches

Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.

The relationship between fibroblast growth and the dynamic stiffnesses of a DNA crosslinked hydrogel

The microenvironment of cells is dynamic and undergoes remodeling with time. This is evident in development, aging, pathological processes, and at tissue-biomaterial interfaces. But in contrast, the majority of the biomimetic materials have static properties. Here, we show that a previously developed DNA crosslinked hydrogel circumvents the need of environmental factors and undergoes controlled stiffness change via DNA delivery, a feasible approach to initiate property changes in vivo, different from previous attempts. Two types of fibroblasts, L929 and GFP, were subject to the alterations in substrate rigidity presented in the hydrogels. Our results show that exogenous DNA does not cause appreciable cell shape change. Cells do respond to mechanical alterations as demonstrated in the cell projection area and polarity (e.g., Soft vs. Soft-->Medium), and the responses vary depending on magnitude (e.g., Soft-->Medium vs. Soft-->Stiff) and range of stiffness changes (e.g., Soft-->Medium vs. Medium-->Stiff). The two types of fibroblasts share specific responses in common (e.g., Soft-->Medium), while differ in others (e.g., Medium-->Stiff). For each cell type, the projection area and polarity respond differently. This approach provides insight into pathology (e.g., cancer) and tissue functioning, and assists in designing biomaterials with controlled dynamic stiffness by choosing the range and magnitude of stiffness change.

Multiscaffold DNA Origami Nanoparticle Waveguides

DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry.

Excitonic AND Logic Gates on DNA Brick Nanobreadboards

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

Simultaneous determination of Young's modulus, shear modulus, and Poisson's ratio of soft hydrogels

Besides biological and chemical cues, cellular behavior has been found to be affected by mechanical cues such as traction forces, surface topology, and in particular the mechanical properties of the substrate. The present study focuses on completely characterizing the bulk linear mechanical properties of such soft substrates, a good example of which are hydrogels. The complete characterization involves the measurement of Youngs modulus, shear modulus, and Poissons ratio of these hydrogels, which is achieved by manipulating nonspherical magnetic microneedles embedded inside them. Translating and rotating these microneedles under the influence of a known force or torque, respectively, allows us to determine the local mechanical properties of the hydrogels. Two specific hydrogels, namely bis-cross-linked polyacrylamide gels and DNA cross-linked polyacrylamide gels were used, and their properties were measured as a function of gel concentration. The bis-cross-linked gels were found to have a Poissons ratio that varied between 0.38 and 0.49, while for the DNA-cross-linked gels, Poissons ratio varied between 0.36 and 0.49. The local shear moduli, measured on the 10 μm scale, of these gels were in good agreement with the global shear modulus obtained from a rheology study. Also the local Youngs modulus of the hydrogels was compared with the global modulus obtained using bead experiments, and it was observed that the inhomogeneities in the hydrogel increases with increasing cross-linker concentration. This study helps us fully characterize the properties of the substrate, which helps us to better understand the behavior of cells on these substrates.

Availability: A Metric for Nucleic Acid Strand Displacement Systems

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only one target DNA strand, catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules.

Kinetics of DNA and RNA Hybridization in Serum and Serum-SDS

Cancer is recognized as a serious health challenge both in the United States and throughout the world. While early detection and diagnosis of cancer leads to decreased mortality rates, current screening methods require significant time and costly equipment. Recently, increased levels of certain micro-ribonucleic acids (miRNAs) in the blood have been linked to the presence of cancer. While blood-based biomarkers have been used for years in cancer detection, studies analyzing trace amounts of miRNAs in blood and serum samples are just the beginning. Recent developments in deoxyribonucleic acid (DNA) nanotechnology and DNA computing have shown that it is possible to construct nucleic-acid-based chemical networks that accept miRNAs as inputs, perform Boolean logic functions on those inputs, and generate as an output a large number of DNA strands that can be readily detected. Since miRNAs occur in blood in low abundance, these networks would allow for amplification without using polymerase chain reaction. In this study, we report initial progress in the development of a DNA-based cross-catalytic network engineered to amplify specific cancer-related miRNAs. Subcomponents of the DNA network were tested individually, and their operation in serum, as well as a mixture of serum with sodium dodecyl sulfate, is demonstrated. Preliminary simulations of the full cross-catalytic network indicate successful operation.