Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations

by

Wilma Olson
Rutgers University

Friday, September 14, 2007
3:30 p.m.–4:30 p.m.
3-180 EE/CS

Making sense of gene repression in living bacteria requires understanding of the looping properties of DNA in crowded, multi-component systems. The presence of HU, a non-specific binding protein that introduces sharp bends and localized untwisting in double-helical DNA, stabilizes functional repression loops as small as ~65 base pairs. As a first step in the analysis of such looping, we have investigated the effects of HU on the configurational properties of short fragments of ideal B DNA, treating the DNA at the level of base-pair steps and incorporating the known effects of HU on DNA structure. We introduce a new sampling technique to model the non-specific binding of HU on DNA and use Monte-Carlo methods to generate three-dimensional configurations of protein-bound DNA. The presentation will focus on properties of small circular duplexes formed in the presence of HU and the implications of these data for the in-vivo looping properties of DNA.

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