Absolute and arbitrary orientation of single molecule shapes

Abstract

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 enables device alignment within 3.2 • on SiO 2 . Orientation is absolute (all degrees of freedom are specified) and arbitrary (every molecule's orientation is independently specified). The use of orientation to optimize device performance is shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration is demonstrated via an array of 3,456 DNA origami with 12 distinct orientations, which indicates the polarization of excitation light.The sequential combination of solution-phase self-assembly (SPSA) and directed self-assembly (DSA) provides a general paradigm for the synthesis of nanoscale devices and their large-scale integration with control circuitry, microfluidics, or other conventionally-fabricated structures. SPSA for the creation of sub-lithographic devices via structural DNA nanotechnology (1) is relatively mature. In particular, typical DNA origami (2) allow up to 200 nanoscale components, including carbon nanotubes (3-5), metal nanoparticles (6, 7), fluorescent molecules (6-8), quantum dots (7, 9) and conductive polymers (10) to be simultaneously juxtaposed at 3-5 nm resolution within a 100 nm×70 nm DNA rectangle. DSA uses topographic (11,12) or chemical (13-26) patterning, fields (27-37), or flow (38-46) to control the higher order structure of molecules and particles. Well-developed for continuous block copolymers films (13, 14), spherical nanoparticles (11, 12), and linear nanostructures (16-22, 27-36, 38-46), DSA is less developed for origami-templated devices for which shape and symmetry play an important role in device function and integration. Two challenges arise in the DSA of orgami-templated devices. The first is analogous to the problem of absolute orientation (47) (Fig. 1A) in computational geometry: Given two Cartesian coordinate systems, what translation and rotation can transform the first to the second? Such transformations are key in computer vision and robotics, where they can be used to plan the motion of a virtual camera, or a robot arm. The physical analog for DSA asks: How can an asymmetric device in solution be positioned and aligned relative to a global reference frame in the laboratory? The second challenge is to achieve absolute orientation for many devices at once, such that the position and alignment of each device is arbitrary, i.e. independent of other devices (Fig. 1B). DNA origami placement (DOP) (24-26) is a potential solution to both challenges. In DOP the * Departments of 1 Bioengineering, 2 Computing & Mathematical Science,

Biotemplated Lithography of Inorganic Nanostructures (BLIN) for Versatile Patterning of Functional Materials

“…In addition, DALI does not yet provide any control over the exact position and orientation of manufactured particles on the substrate, which is required, for example, in advanced metasurface fabrication. 23,25 Here, we address the major limitations of the original DALI protocol and introduce a completely new technique dubbed biotemplated lithography of inorganic nanostructures (BLIN) (see Figure 1). We show that besides DNA nanostructures, other self-assembled nanoscale shapes can be equally employed in molecular patterning.…”

DNA Nanotechnology Meets Nanophotonics

“…Rather, I would like to end this paragraph by highlighting the recent groundbreaking works by Paul Rothemund's group, who has combined the respective strengths of both DNA nanotechnology and lithographic patterning to map nanocavity emission via precision placement of DNA origami 9 as well as to optimize nanophotonic device performance via control over the fluorescent dipole orientations using DNA origami. 10 So what do we aim for 20 years along the road? For fundamental research, smart strategies need to be developed for creation of large DNA origami templates to accommodate Published: November 6, 2020…”