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Topological analysis of enzymatic actions: DNA link formation by Xer recombination and DNA unknotting by type II topoisomerase.
by
Mariel Vazquez
Mathematics Department, U.C. Berkeley
Coauthors: De Witt Sumners, Sean D. Colloms and Javier Arsuaga
DNA topology is the study of geometrical (supercoiling) and topological (knotting) properties of DNA loops and circular DNA molecules. Virtually every reaction involving DNA is influenced by DNA topology, or has topological effects. Site-specific recombinases and topoisomerases are enzymes able to change the topology of circular DNA by breaking the DNA and introducing one or more crossing changes. Mathematical analysis of such changes may provide relevant information about the possible enzymatic pathways, and about DNA conformation at the moment of double-stranded break induction. In this talk I will discuss some of the problems that I am currently interested in, and the topological tools used in their analyses.
First I will talk about Xer recombination and how we applied, and extended, the tangle model for site-specific recombination to propose a unique enzymatic mechanism. I will then present the Java applet TangleSolve that makes the tangle model easily accessible to the interested molecular biologist. Finally, if time permits I will talk about our recent work on DNA unknotting by type II topoisomerase.
Date received: October 13, 2004
Copyright © 2004 by the author(s). The author(s) of this work and the organizers of the conference have granted their consent to include this abstract in Topology Atlas. Document # capf-08.