Measuring internal forces in single-stranded DNA: Application to a DNA force clamp

TL;DR

This paper introduces a novel method for calculating internal forces in DNA using coarse-grained models, demonstrated with the oxDNA model, revealing insights into force estimation pitfalls and emphasizing the importance of secondary structure and ionic conditions.

Contribution

The paper presents a new framework for calculating internal forces in DNA structures, applicable to various biomolecular systems and models.

Findings

Identified limitations of conventional elastic polymer models.

Showed the impact of secondary structure and ionic conditions on DNA elasticity.

Demonstrated the method on a nanoscopic force clamp.

Abstract

We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model potentials, and using our framework, internal forces are calculated for two simple DNA systems and for a recently-published nanoscopic force clamp. Our results highlight some pitfalls associated with conventional methods for estimating internal forces, which are based on elastic polymer models, and emphasise the importance of carefully considering secondary structure and ionic conditions when modelling the elastic behaviour of single-stranded DNA. Beyond its relevance to the DNA nanotechnological community, we expect our approach to be broadly applicable to calculations of internal force in a variety of structures -- from DNA to protein -- and across other coarse-grained simulation models.