Asymmetric DNA Shapes for Orienting Molecular Components within Hybrid Nanodevices

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A key problem is the scalable manufacturing of "hybrid nanodevices" which combine a conventionally-fabricated optical or electronic device with an unconventional component, such as a single molecule or nanoparticle. The unconventional component has some sought-after property, but it is too small to function on its own, and the conventionally-fabricated device connects the unconventional component to the larger world. Applications include the incorporation of quantum dots into electronics for flat panel displays, or into optical chips for quantum computers or telecommunications. Biological applications include the incorporation of single proteins or DNA into sensors for diagnostics or genome sequencing. Current methods for creating hybrid devices are too expensive, and have low yields. Research under this award combines experimental DNA nanotechnology, theoretical computational geometry, and conventional microfabrication to develop novel fabrication techniques that will bring prototype hybrid nanodevices out of the laboratory and enable them to be inexpensively produced at industrial-scale. Techniques developed under this award will be spread through the greater research community via collaborations and tutorial workshops. This research will be shared with women and minority high school students through student visiting days at the laboratory, and reciprocal researcher visits to high school classrooms, to stimulate their participation in STEM fields. Scientists have long relied on random processes to integrate single molecules and nanoparticles with microfabricated devices. This has allowed them to demonstrate the extraordinary performance of unconventional components, but only for a few prototype devices. Recently, the directed self-assembly of DNA origami shapes onto lithographically-patterned binding sites has allowed the reliable positioning of single molecules or nanoparticles at precise locations within microfabricated devices. However, the use of symmetric DNA triangles has limited the technique to simple point-like components, preventing the integration of components which must be precisely oriented, such as molecular rectifiers. This research will design, simulate, synthesize, and experimentally test asymmetric DNA shapes capable of precisely orienting their cargo onto lithographic binding sites. Numerical energy landscape analysis will be used to identify promising asymmetric shapes, and analytic proofs will be constructed to confirm that their binding landscapes have no local minima. A major intellectual contribution will be guidelines and principles for designing binding sites and energy landscapes for directed self-assembly. The high-yield fabrication of thousands of bipolar or multipolar devices based on carbon nanotubes and polarization-dependent fluorescent dyes will demonstrate the practical and scalable integration of complex, asymmetric components into hybrid nanodevices.