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 repositiong through one-basepair twist defects and through ten-basepair
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 orientiation, temperature
and DNA anisotropy. Having this mobility at hand we speculate about the
interaction between a nucleosome and a transcribing RNA polymerase and suggest
a novel mechanism that might account for polymerase induced nucleosome
repositioning.Comment: 23 pages, 4 figures, submitted to J. Mol. Bio
