DNA nanotechnology: understanding and optimisation through simulation

TL;DR

This paper reviews the current state of DNA nanotechnology, emphasizing the role of simulation models like oxDNA in understanding and optimizing nanoscale self-assembly and dynamic systems, with new insights into mechanical tension effects.

Contribution

It introduces the use of coarse-grained models such as oxDNA for detailed simulation of DNA nanostructures and demonstrates how mechanical tension can significantly improve nanomechanical device performance.

Findings

Mechanical tension accelerates walker recovery by 3-4 orders of magnitude.

Simulation reveals the interplay of kinetic, thermodynamic, and mechanical factors.

Biasing strand-displacement processes can control reaction rates.

Abstract

DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.