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).
Jointly with John
Luecke and Isabel Darcy, I
have analyzed data from novel difference topology experiments to
unveil the structure of the Mu transpososome. The technique was
developed in Rasika
Harshey’s and Makkuni
Jayaram’s lab, and the experiments were done by Shailja
Pathania.
The tangle model is a mathematical method due to De Witt
Sumners and Claus Ernst [Sumners et al. Quart. Rev.
Biophysics 28, 3 (1995), 253 - 313], which uses knot theory and
low-dimensional topology to understand the mechanisms of binding
and strand-exchange by site-specific recombinases. A web
description of the tangle model can be found here.
