Modeling DNA unknotting by type II topoisomerases

Friday, October 26, 2007 - 11:15am - 12:15pm
Lind 409
Mariel Vazquez (San Francisco State University)
Type II topoisomerases simplify DNA knots and links efficiently by performing strand-passage on DNA strands. Experimental studies have shown that these enzymes simplify the topology of DNA below thermodynamical equilibrium, however the key behind their efficiency is yet to be revealed. Motivated by these experimental observations, we study random transitions of knotted polygonal chains of fixed length. We use Monte Carlo computer simulations and computational knot theory methods to model strand-passage, with and without topological biases, on the knotted chains and to identify the resulting knotting probabilities.

This project is funded by NIH MBRS SCORE grant S06 GM052588.