The Mathematics of Site-specific Recombination: 1. Difference Topology<br/><br/>Experiments and the Mu Tranpososome; 2. DNA Unlinking by XerCD/FtsK

Friday, September 21, 2007 - 10:30am - 11:30am
EE/CS 3-180
Mariel Vazquez (San Francisco State University)
DNA topology is the study of geometrical (supercoiling) and
topological (knotting) properties of DNA loops and circular DNA
molecules. Multiple cellular processes, such as DNA replication and
transcription, affect the topology of DNA. Controlling these changes
is key to ensuring stability inside the cell. Changes in DNA topology
are mediated by enzymes such as topoisomerases and site-specific
recombinases. We have successfully used techniques from knot theory
and low-dimensional topology, aided by computational tools, to analyze
the action of site-specific recombinases. I will introduce the tangle
model and report on two recent analyses:

1. Based on the difference topology experimental results of Pathania,
Jayaram, and Harshey (Cell, 2002), we solve 3-string tangle equations
to understand the topological structure of DNA within the Mu
transpososome. Pathania et al. (2002) proposed one 3-string tangle
model for the Mu transpososome. We describe other families of
solutions to the same tangle equations and we argue that the model
given by Pathania et al. (2000) is the only biologically reasonable

2. The FtsK-XerCD system has been to successfully unlink complicated
DNA catenanes produced by lambda Int and by DNA replication. We use
tangles to argue that a stepwise unlinking by multiple recombination
steps is the only plausible mechanism of action.