Brownian Dynamics Simulation of DNA Unrolling from the Nucleosome

Abstract

Nucleosomes organize chromatin in eukaryotic cells at the lowest scale by wrapping the DNA double helix around a histone octamer. The mechanism by which this structure can be opened, giving access to DNA-processing enzymes, is of fundamental biological importance. Here we describe a new coarse-grained model based on the toroidal geometry of the nucleosome which allows the simulation of nucleosome stretching experiments with a Brownian dynamics algorithm including hydrodynamics. We obtain force-extension curves and calculate energy barriers and kinetic rate constants of the unrolling transition from rupture forces.