Phys. Rev. Lett. 97, 208102 (2006) [4 pages]Kinetic Accessibility of Buried DNA Sites in NucleosomesReceived 12 May 2006; published 14 November 2006 Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the “semiflexible Brownian rotor.” © 2006 The American Physical Society URL:
http://link.aps.org/doi/10.1103/PhysRevLett.97.208102
DOI:
10.1103/PhysRevLett.97.208102
PACS:
87.15.He, 36.20.Ey, 87.16.Sr
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