Research Article

Absolute and arbitrary orientation of single-molecule shapes

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Science  19 Feb 2021:
Vol. 371, Issue 6531, eabd6179
DOI: 10.1126/science.abd6179

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Orienting origami binding

Directing self-assembly for devices will require placing nanocomponents not only in the correct position on a surface but also in particular orientations. Gopinath et al. designed an asymmetric DNA origami, a “small moon” shape that binds to lithographically patterned sites on silica to within 3° of a target orientation angle. The authors were able to position and orient a molecular dipole within the resonant mode of an optical cavity. More than 3000 DNA origami were arranged in a single fabrication step in 12 different orientations to create a simple polarimeter.

Science, this issue p. eabd6179

Structured Abstract


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.


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.


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.


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.

Directed self-assembly of asymmetric DNA origami shapes enables orientation-controlled integration of chemically synthesized nanodevices with conventionally fabricated microdevices.

Top: How can one transfer thousands of nanodevices to a surface and fix each with its own orientation independent of the others? Middle left: Naïvely, an asymmetric right triangle (dark purple) carrying a device could orient the device by sticking to a surface binding site (green) of the same shape. But such triangles often bind incorrectly because there are multiple minima in the energy landscape (E). Middle right: The landscape for a disk with an offset hole (small moon, light purple) has a single minimum; thus, a small moon binds its site with a unique orientation. Bottom: The intensity of light emitted by a photonic crystal cavity microdevice (left) can be optimized (right) when small moons are used to align fluorescent molecule nanodevices (red arrow) with the polarization of the cavity mode.


DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is challenging: Large numbers of freely diffusing devices must be fixed at desired locations with desired alignment. We present a DNA origami molecule whose energy landscape on lithographic binding sites has a unique maximum. This property enabled device alignment within 3.2° on silica surfaces. Orientation was absolute (all degrees of freedom were specified) and arbitrary (the orientation of every molecule was independently specified). The use of orientation to optimize device performance was shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration was demonstrated with an array of 3456 DNA origami with 12 distinct orientations that indicated the polarization of excitation light.

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