Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length

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...

Full description

Saved in:
Bibliographic Details
Published in:Physical review letters 2023-02, Vol.130 (5), p.058402-058402, Article 058402
Main Authors: Gutiérrez Fosado, Yair Augusto, Landuzzi, Fabio, Sakaue, Takahiro
Format: Article
Language:English
Subjects:
Base Pairing
DNA
Elasticity
Molecular Dynamics Simulation
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0031-9007
1079-7114
DOI:10.1103/PhysRevLett.130.058402