Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: octamer repositioning through one-base-pair twist defects and through ten-base-pair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study, we give a quantitative theory for nucleosome repositioning in the presence of such ligands. We show that the experimentally observed octamer mobilities are consistent with the picture of bound ligands blocking the passage of twist defects through the nucleosome. This strongly supports the model of twist defects inducing a corkscrew motion of the nucleosome as the underlying mechanism of nucleosome sliding. We provide a theoretical estimate of the nucleosomal mobility without adjustable parameters, as a function of ligand concentration, binding affinity, binding site orientation, temperature and DNA anisotropy. Having this mobility in hand, we speculate on the interaction between a nucleosome and a transcribing RNA polymerase, and suggest a novel mechanism that might account for polymerase-induced nucleosome repositioning on short DNA templates.

In this paper, we analyze the behavior of hydrophobic polyelectrolytes. It has been proposed that this system adopts a pearl necklace structure reminiscent of the Rayleigh instability of a charged droplet. Using a Poisson-Boltzmann approach, we calculate the counterion distribution around a given pearl, assuming the latter to be penetrable for the counterions. This allows us to calculate the effective electric charge of the pearl as a function of the chemical charge. Our predictions are in good agreement with the recent experimental measurements of the effective charge by Essafi et al. (Essafi, W.; Lafuma, F.; Baigl, D.; Williams, C. E. Europhys. Lett. 2005, 71, 938.). Our results allow us to understand the large deviation from the Manning law observed in these experiments.