Coarse-graining DNA for simulations of DNA nanotechnology

TL;DR

This paper reviews coarse-grained DNA models, especially OxDNA, for simulating DNA nanotechnology processes, enabling systematic studies of self-assembly and biophysical properties at larger scales.

Contribution

It introduces and discusses the OxDNA model as a powerful tool for simulating DNA nanotechnology at coarse-grained levels, facilitating new insights.

Findings

OxDNA enables simulation of DNA self-assembly.

The model provides insights into DNA biophysical properties.

Applications span various DNA nanotechnology systems.

Abstract

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.