Stochastic model for nucleosome sliding in the presence of DNA ligands

TL;DR

This paper introduces a stochastic three-state model to describe nucleosome sliding along DNA, accounting for the presence of DNA ligands, and provides analytical solutions validated by simulations.

Contribution

The model offers a novel analytical framework for understanding nucleosome mobility influenced by DNA ligands, extending previous models to include ligand effects.

Findings

Analytical solutions match numerical simulations accurately.

Ligands significantly alter nucleosome diffusion dynamics.

External forces impact nucleosome movement differently with ligands present.

Abstract

Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic three-state model for the diffusion of a nucleosome along DNA in the presence of such ligands. It allows us to describe the dynamics and the steady state of such a motion analytically. The analytical results are in excellent agreement with numerical simulations of this stochastic process.With this model, we study the response of a nucleosome to an external force and how it is affected by the presence of ligands.