A theory of DNA dissociation from the nucleosome

Previous analysis of an elastic model of the nucleosome indicated that 10 bp end segments of DNA can exist in a continuum of mechanically stable trajectories ranging from complete winding on the histone octamer to complete unwinding. Stable states of 20 bp and 40 bp end segments, however, are grouped in bands separated by gaps where DNA trajectories are unstable. We extend these results to cover the entire range up to a complete nucleosomal turn, 80 bp. We find that 10 to 60 bp segments have states intermediate between fully wound and fully unwound that are mechanically stable. In striking contrast, there is no stable intermediate trajectory for 70 bp or 80 bp segments. Segments of these lengths constitute a two-state system. A 70 or 80 bp segment is either fully wound or fully unwound, and the population of these states is governed by Boltzmann's thermal distribution. We have found a plausible dissociation pathway from the fully wound to the fully unwound state for the 80 bp segment. In a ponderous breathing motion that breaks all contacts with the histone ponderous breathing motion that breaks all contacts with the histone surface, the segment climbs to an activation peak of about 12 kcal/mol, then rapidly straightens away from the histone core to complete dissociation.