Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Motivated by recent experiments on nucleosome accessibility [1,2] we study the transient exposure of protein-binding DNA sites within nucleosomes using a theoretical model for spontaneous partial DNA unwrapping from histones. We focus on the functional dependence of the rates for site exposure and re-burial on the site position, which is pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection however reveals a surprising dependence of the re-burial rates on the length of unwrapped DNA. We show that this corresponds to a physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the {\it semiflexible Brownian rotor}.\newline [1] G. Li, M. Levitus, C. Bustamante, and J. Widom, Nat. Struct. Biol. {\bf 12}, 46 (2005)\newline [2] M. Tomschik, H. Zheng, K. van Holde, J. Zlatanova, and S. Leuba, Proc. Natl. Acad. Sci. U.S.A. {\bf 102}, 3278 (2005)\newline [3] W. M\"obius, R.A. Neher, and U. Gerland, Phys. Rev. Lett. {\bf 97}, 208102 (2006)