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Published February 19, 2021 | Supplemental Material + Submitted
Journal Article Open

Absolute and arbitrary orientation of single-molecule shapes


Introduction: Molecular and particulate nanodevices such as carbon nanotubes and semiconductor nanowires exhibit properties that are difficult to achieve with conventional silicon microfabrication. Unfortunately, most such devices must be synthesized or processed in solution. To combine nanodevices into larger circuits, or simply to connect them with the macroscopic world, scientists use a range of directed self-assembly techniques to deposit them at specific locations on microfabricated chips. Many such methods work well with spherical devices for which orientation is irrelevant. For linear wire-like devices, flow or field alignment works for applications involving a single global orientation. However, a general solution for multiple orientations or less symmetric devices (e.g., diodes or transistors) has remained elusive. Rationale: Single-molecule DNA origami shapes can simultaneously act as templates to create nanodevices and as adaptors to integrate them onto chips. With 200 attachment sites just 5 nm apart, origami can organize any material that can be linked to DNA; for example, carbon nanotube crosses have been templated to yield field-effect transistors. With ~100-nm outlines, origami are large enough that shape-matched binding sites can be written at arbitrary positions on chips using electron-beam lithography. Our prior work used equilateral triangles that stuck to binding sites in six degenerate orientations. Here, we asked whether origami shapes could provide both absolute orientation (to uniquely orient asymmetric devices) and arbitrary orientation (to independently orient each device). Success depended on finding a suitably asymmetric shape. Results: To break up-down symmetry and to ensure that each shape was deposited right-side up, we added adhesion-decreasing single-stranded DNAs to one side of each origami. The binding of asymmetric right triangles to shape-matched sites gave orientation distributions consistent with strong kinetic trapping, as predicted by the volumes of basins of attraction around local minima. This motivated the design of a "small moon" shape whose energy landscape has a single minimum. Fluorescent molecular dipoles fixed to small moons served as model nanodevices and allowed us to measure variability in orientation (±3.2°) by polarization microscopy. Large-scale integration was demonstrated by an array of 3456 small moons in 12 orientations, which we used as a fluorescence polarimeter to indicate excitation polarization. The utility of orientation for optimizing device performance was shown by aligning fluorescent dipoles within microfabricated optical cavities, which showed a factor of 4.5 increase in emission. Conclusion: Control over optical dipole orientation may enable metal nanorod metasurfaces at visible wavelengths, optimized coupling of emitters to nanoantennas, lumped nanocircuits, and coherence effects between small numbers of emitters. Still, these applications and the devices we present do not demonstrate the full power of the small moons: Dipolar devices can rotate 180° and still function. Completely asymmetric nanodevices requiring absolute orientation (e.g., molecular bipolar junction transistors) have yet to be developed; now that orientation can be controlled, there is motivation to invent them. In the meantime, the wiring of existing devices into circuits may be greatly simplified.

Additional Information

© 2021 American Association for the Advancement of Science. This is an article distributed under the terms of the Science Journals Default License. Received 2 July 2020; accepted 14 December 2020. Fabrication was done at Caltech's Kavli Nanoscience Institute. Funding: Supported by Office of Naval Research awards N00014-14-1-0702 and N00014-17-1-2610, NSF grants 1636364 and 1317694 (Expedition in Computing, Molecular Programming Project, http://molecular-programming.org), Air Force Office of Scientific Research grant FA9550-16-1-0019 (A.M.), the Natural Sciences and Engineering Research Council of Canada (D.K.), a Banting Fellowship (C.T.), the Orr Family Foundation, and the Abedin Institute. Author contributions: A.G. and A.M. performed all experiments; A.G. performed Lumerical simulations; A.G. and P.W.K.R. analyzed primary experimental data; C.T. wrote software for thermodynamic and kinetic modeling and simulation; C.T. and P.W.K.R. performed analysis and comparison of experimental data with thermodynamic and kinetic predictions; C.T. and D.K. derived the small moon shape; A.G. and P.W.K.R. wrote the manuscript; and all authors edited the manuscript. Competing interests: A.G., C.T., D.K., and P.W.K.R. have filed a patent application based on this work. A.G. and P.W.K.R. are co-founders of Palamedrix. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper or the supplementary materials. Software for kinetic, thermodynamic, and EM simulations, right triangle orientation analysis, as well as e-beam and DNA origami design files are present in the supplementary materials and on Zenodo (62).

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Submitted - 1808.04544.pdf

Supplemental Material - abd6179_Gopinath_SM.pdf


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August 20, 2023
October 18, 2023