A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

TL;DR

This paper introduces a highly efficient, single nucleotide resolution mesoscopic model for double-stranded DNA that can simulate large molecules over relevant time scales, aiding research in DNA nanotechnology and biology.

Contribution

The paper presents a novel, scalable DNA model that maintains helical structure and enables large-scale, long-time simulations with high computational efficiency.

Findings

Model accurately reproduces experimental force and torque responses.

Simulates DNA denaturation kinetics effectively.

Supports large-scale DNA simulations up to a million base pairs.

Abstract

The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules -- up to a million base pairs -- for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. We compare the behaviour of our model with single molecule experiments where dsDNA is manipulated by external forces or torques. We also present some results on the kinetics of denaturation of linear DNA.