Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

TL;DR

This study introduces simple elastic network models for DNA that effectively analyze sequence-dependent dynamics, revealing correlations between DNA flexibility and nucleosome formation potential.

Contribution

The paper presents both all-atom and coarse-grained elastic network models that accurately reproduce DNA dynamics based on sequence geometry, enabling exhaustive analysis of long DNA sequences.

Findings

Positive correlation between nucleosome-forming ability and inter-strand fluctuation strength.

Effective reproduction of detailed DNA dynamics with a coarse-grained model.

Exhaustive analysis of long DNA sequences (~150 bp) dynamics.

Abstract

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately $\sim 150$ bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.