Fig. 5

Molecular Dynamics simulations of nucleosomal DNA. Panel a Molecular Dynamics simulations of the conformational space of the D (green) and A (red) dyes in an extended nucleosomal DNA duplex [D strand (dark blue), A strand (light blue)]. Panel b Nucleosome viewed from top (Left) and from the side (Right), based on known crystal structures. Only the core of the histone (magenta) is shown for simplicity. The solid line connects the centers of mass of the fluorophores’ accessible space. Adapted from [28] with written permission given by the original license holders