DNA Topology
Type 2 Topoisomerases

I am very interested in understanding the mechanism of action of type-2 topoisomerases. I am currently modelling their DNA unknotting reaction. This project was inspired by our work on DNA packing in bacteriophages (Arsuaga et al. 2002) while working with Javier Arsuaga and Joaquim Roca (molecular biologist). The theoretical part took off as an undergraduate project involving several Berkeley undergraduates: first Barath Raghavan (now a CS graduate student at UCSD). Since then several students have worked on the project: Diana Nguyen (UCLA Medical School), Miki Suga and Xia (Carol) Hua (MIT), Nathan Shayefar (UCB), Itamar landau (UCB), Janella Slaga (SFSU), Juliet Portillo (SFSU), Ben Dalziel (SFSU), Nicholas Normandin (SFSU), Andrew Herrmann (SFSU), Reuben Brascher (SFSU), Jeff halperin (SFSU). We use knot theory and computer simulations to model strand-passage on polygonal chains (the DNA) in space. You can see a description of the early stages of the project in [Hua et al, 2007; Hua and Vazquez, 2007]. More papers are in preparation. 

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