Brownian dynamics simulation of the interaction between DNA and histone

In all eukaryotes, DNA wraps around a histone octamer in a left-handed way, forming a stable nucleosome structure. We numerically study the interaction between DNA and histone using a Brownian dynamics simulation. The process of nucleosome formation is shown in detail. We propose a histone octamer rotation model for the process of nucleosome formation. By simulating the stretching of a nucleosome chain we obtain the force versus extension and extension versus time curves, which are found to be consistent with experimental results. The process of chirality formation of a nucleosome is studied by building up a histone octamer model with a quantitatively adjustable chirality, and the chirality is found to be strongly dependent on the chirality of the histone octamer. We also show that the nucleosome chirality may be broken at elevated temperatures.