Prof. Manoel Manghi, Laboratoire de Physique Théorique, Université Paul Sabatier, Toulouse, France
DNA denaturation bubbles are made of several consecutive open base-pairs in double-stranded DNA. Although they occur with a very low probability in a free DNA in solution at physiological temperature, their role is central for biological functions such as transcription or DNA compaction.
Using theoretical arguments and Brownian dynamics simulations, I will show how torsional degrees of freedom play a key role in their closure and nucleation dynamics. In particular, using metadynamics, we obtain opening times scales on the millisecond range and long closure times of several microseconds for bubbles larger than about 10 base-pairs, as observed in in vitro experiments.
Jul 10, 2014 | 04:15 PM