The Effect of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-closure Properties of DNA Deduced from Monte Carlo Simulation<br/><br/><br/><br/>

Thursday, September 20, 2007 - 5:00pm - 5:15pm
EE/CS 3-180
Luke Czapla (Rutgers, The State University Of New Jersey )
Joint work with David Swigon and Wilma K Olson (PI).

A recently developed Monte Carlo technique for calculating the cyclization propensity of DNA chains has been modified to consider the effect of proteins which bind randomly to the double helix. The method is applied to consider the bacterial nucleoid protein HU, known to bind non-specifically to unmodified double-helical DNA. We simulate chains with a fixed average number of bound protein, with proteins placed in random positions. Our results predict that not only will HU greatly enhance DNA cyclization, as measured by the J factor, but that the effect of helical repeat is greatly reduced and the J factor is nearly constant over a wide range of chain lengths. Moreover, HU induces negative supercoiling which condenses the DNA, consistent with the requirement of HU for bacterial nucleoid condensation. The mechanism of sharp bending and significant untwisting of HU-bound DNA is common among proteins known to restore this nucleoid condensation. Mathematical and computational techniques involved in the Monte Carlo simulation of DNA will be discussed.