Length scale dependent elasticity in DNA from coarse-grained and all-atom models

TL;DR

This paper demonstrates that off-site interactions in DNA, captured through coarse-grained and all-atom models, lead to length scale dependent elasticity, improving the understanding of DNA mechanics beyond local elastic theories.

Contribution

It introduces an analytical framework to estimate length scale dependent bending and torsional persistence lengths considering off-site couplings in DNA.

Findings

Off-site interactions cause length scale dependence in DNA elasticity.

Simulations show strong off-site couplings for certain degrees of freedom.

Theory predicts significant length scale effects in torsional fluctuations, consistent with experiments.

Abstract

The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are coupled. Hence, off-site models provide a more realistic description of the mechanics of the double helix. We show that off-site interactions are responsible for a length scale dependence of the elasticity, and we develop an analytical framework to estimate bending and torsional persistence lengths in models including these interactions. Our simulations indicate that off-site couplings are particularly strong for certain degrees of freedom, while they are very weak for others. If stiffness parameters obtained from DNA data are used, the theory predicts large length scale dependent effects for torsional fluctuations and a modest effect in bending fluctuations, which is in agreement with experiments.