Kinetic accessibility of buried DNA sites in nucleosomes.
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."
Möbius
Wolfram
W
Arnold Sommerfeld Center for Theoretical Physics and Center for Nanoscience, LMU München, Theresienstrasse 37, 80333 München, Germany.
Neher
Richard A
RA
Gerland
Ulrich
U
D001703:Biophysics / Q000379:methods*; D003460:Crystallization; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D006657:Histones / Q000737:chemistry*; D007700:Kinetics; D015233:Models, Statistical; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry; D013997:Time Factors
D006657:Histones; D009707:Nucleosomes; D011108:Polymers; D004247:DNA