The Topology of DNA-Protein Interactions

The central axis of the famous DNA double helix can become knotted
or linked as a result of numerous biochemical processes, most notably
site-specific recombination. Site-specific recombinases are naturally
occurring enzymes that cleave and reseal DNA molecules in very precise ways.
As a by product of their main purpose, they manipulate cellular DNA in
topologically interesting and non-trivial ways. So if the axis of the DNA
double helix is circular, these cut-and-seal mechanisms can be tracked by
corresponding changes in the knot type of the DNA axis.  In this talk, I'll
explain several topological strategies to investigate these biological
situations. As a concrete example, I will disscuss my recent work, which
predics what types of DNA knots and links can arise from site-specific
recombination on DNA twist knots.