The Brownian and Flow‐Driven Rotational Dynamics of a Multicomponent DNA Origami‐Based Rotor

Abstract

Nanomechanical devices are becoming increasingly popular due to the very diverse field of potential applications, including nanocomputing, robotics, and drug delivery. DNA is one of the most promising building materials to realize complex 3D structures at the nanoscale level. Several mechanical DNA origami structures have already been designed capable of simple operations such as a DNA box with a controllable lid, bipedal walkers, and cargo sorting robots. However, the nanomechanical properties of mechanically interlinked DNA nanostructures that are in general highly deformable have yet to be extensively experimentally evaluated. In this work, a multicomponent DNA origami‐based rotor is created and fully characterized by electron microscopy under negative stain and cryo preparations. The nanodevice is further immobilized on a microfluidic chamber and its Brownian and flow‐driven rotational behaviors are analyzed in real time by single‐molecule fluorescence microscopy. The rotation in previous DNA rotors based either on strand displacement, electric field or Brownian motion. This study is the first to attempt to manipulate the dynamics of an artificial nanodevice with fluidic flow as a natural force.

Unified Nanotechnology Format: One Way to Store Them All

“…There are some workarounds, however, to achieve lattice structures where all lattices have the same arrangement. However, well-defined support for this kind of design is missing, despite this being a topic for many researchers [ 39 , 40 , 41 , 42 ]. In contrast, UNF was designed with a multi-component design in mind, naturally supporting such structures.…”

“…Another example of multi-component design is the DNA origami rotor structure, visualized in Figure 8 , proposed by Ahmadi et al [ 42 ]. This structure consists of four lattice-based components (three honeycombs, one square), which can be stored entirely in UNF.…”

“… DNA origami rotor [ 42 ] together with an antibody (PDB: 1IGY [ 43 ]), visualized in oxView. An example of a multi-component DNA-protein hybrid design, which can be stored in UNF.…”

Double‐ to Single‐Strand Transition Induces Forces and Motion in DNA Origami Nanostructures

“…The main molecular interactions employed to control motion on the nanoscale are DNA hybridization (mainly toehold‐mediated strand displacement) and base stacking. Examples of such motion controlled by molecular interactions include reconfigurable plasmonic devices, [ 19 ] hinges, [ 20,21 ] tweezers, [ 18,22 ] rotary devices, [ 23–26 ] walkers, [ 27 ] drug carriers [ 28,29 ] and robots sorting molecules or nanoparticles. [ 30,31 ] Other molecular interactions as driving mechanisms include target molecule binding [ 32,33 ] and aptamer [ 28,29 ] as well as nucleosome interactions.…”

A nanoscale reciprocating rotary mechanism with coordinated mobility control

“…The construction of artificial molecular machines by chemical synthesis has previously provided important insights regarding how to create molecular mechanisms with internal degrees of freedom, such as catenanes and rotaxanes, and how to power molecular motions using chemical fuels, light, and other stimuli 6 – 12 . DNA nanotechnology has also already provided a range of mechanical systems including pivots, hinges, crank sliders, and rotary mechanisms 13 – 17 that can be reconfigured using strand displacement reactions (SDR) 18 or by changing environmental parameters such as pH, ionic strength, temperature, and external fields 19 – 24 .…”