Characterization And Probability Of DNA Unlinking Pathways By XerCD-FtsK Enzymes

Simplifying the topology of DNA is essential to cellular processes such as DNA replication. Knotted and linked DNA causes complications when it needs to be copied (DNA replication) and transcribed into RNA. DNA topology simplification is usually mediated by topoisomerases (e.g. Topo IV from Escherichia coli). In E. coli, in the absence of topo IV, the XerCD-FtsK complex has been found to effectively unlink replication links. Knot theory and tangle calculus offer methods that can be used to understand how enzymes can change the topology of DNA. We are interested in characterizing all possible recombination pathways taking a specific link to the unlink by the XerCD-FtsK enzymes. Our group is using topological methods to enumerate all the possible pathways of unlinking of this enzyme. We also want to assign probabilities to these pathways. We use a Monte Carlo algorithm in a suite of computational tools called RECOMBO to address this problem. In this poster I will give an overview of both the mathematical and computational methods used in the analysis of XerCD-FtsK. I will also discuss the method, using RECOMBO, to estimate the most probably DNA unlinking pathway.