Dresden 2006 – scientific programme

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AKB: Biologische Physik

AKB 6: DNA Mechanics

AKB 6.4: Talk

Monday, March 27, 2006, 15:15–15:30, ZEU 260

The effect of semiflexibility on the dynamics of DNA in nucleosomes — •Wolfram Möbius, Richard A. Neher, and Ulrich Gerland — Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for Nanoscience (CeNS), LMU München

Even though the DNA in eukaryotic cells is tightly packed with the help of histones, it must be accessible for passively binding regulatory proteins. According to the site exposure mechanism [1], these proteins can temporarily gain access to a buried DNA site during conformational fluctuations of nucleosomes, the fundamental packing units consisting of about 150 base pairs of DNA wrapped around a histone complex. Recently, the dynamics of spontaneous partial DNA unwrapping was observed directly, using optical single molecule techniques [2,3]. Here, we study this dynamics within a mesoscopic model of the nucleosome, using Brownian dynamics simulations and theoretical analysis of simplified toy models. We find that the internal polymer dynamics of the semiflexible DNA has a strong impact on the dynamics of our nucleosome model. We characterize this effect in detail and discuss a number of experimentally relevant predictions of our model.

[1] Polach and Widom, Journal of Molecular Biology 254, 130 (1995)

[2] Li et al., Nature Structural & Molecular Biology 12, 46 (2005)

[3] Tomschik et al., PNAS 102, 3278 (2005)