Coarse-graining DNA: Symmetry, non-local elasticity and persistence length

TL;DR

This paper develops a systematic coarse-graining approach for DNA, linking microscopic parameters to macroscopic elastic properties and revealing new couplings affecting DNA's mechanical behavior at different scales.

Contribution

It introduces a novel scheme connecting base-pair scale parameters to persistence length, incorporating off-site couplings and scale-dependent elastic moduli.

Findings

Identification of relevant couplings between degrees of freedom.

Clarification of scale dependence of elastic moduli.

Revealing previously unnoticed off-site couplings.

Abstract

While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off site couplings between deformations with different parity.