Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Details Kinetic Accessibility of Buried DNA Sites in Nucleosomes Kinetic Accessibility of Buried DNA Sites in Nucleosomes

2006-05-11

arxiv.org/abs/q-bio/0605017v3

Phys. Rev. Lett. 97, 208102 (2006)

Biology

Quantitative Biology

Subcellular Processes

final version as published in Phys. Rev. Lett

Scientific paper

10.1103/PhysRevLett.97.208102

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."

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