Brownian dynamics studies of DNA internal motions

Abstract

Earlier studies by Chow and Skolnick suggest that the internal motions of bacterial DNA may be governed by strong forces arising from being crowded into the small space of the nucleoid, and that these internal motions affect the diffusion of intranuclear protein through the dense matrix of the nucleoid. These findings open new questions regarding the biological consequences of DNA internal motions, and the ability of internal motions to influence protein diffusion in response to different environment factors. The results of diffusion studies of DNA based on coarse-grained simulations are presented. Here, our goals are to investigate the internal motions of DNA with respect to external factors, namely salt concentration of the solvent and intranuclear protein size, and to understand the mechanisms by which proteins dif- fuse through the dense matrix of bacterial DNA. First, a novel coarse-grained model of the DNA chain was developed and shown to maintain the fractal property of in vivo DNA. Next, diffusion studies using this model were performed through Brownian dynamics simulations. Our results suggest that DNA internal motions may be substantially affected by ion concentrations near physiological ion concentration ranges, with the diffusion activity increasing to a limit with increases in ion concentration. Furthermore, it was found that, for a fixed protein volume fraction, the motions of proteins in a DNA-protein system are substantially affected by the size of the proteins, with the diffusion activity increasing to a limit with decreasing protein radii, but the internal motions of DNA within the same system do not appear to change with changes to protein sizes.