DNA Knots

Topological characterization of knots and links arising from site-specific recombination on twist knot substrates

speaker: Karin Valencia (Imperial College)

abstract: Site-specific recombination is an important cellular process that often changes the topology of the central axis of the underlying DNA molecule, the substrate. This cellular reaction on supercoiled circular knotted or unknotted DNA yields a variety of knotted or linked molecules, products. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. Twist knots are also ubiquitous in DNA since in the cell most DNA is (plectonemically) supercoiled (like an overused phone cord) and in the lab most experiments done with site-specific recombinases use small (plectonemically) supercoiled circular DNA molecules, so an unknot can be transformed to a twist knot by a single crossing change.

Using knot theoretic techniques, we model site-specific recombination on the very common twist knot substrates, and completely characterize all possible products. We will briefly explain both the assumptions and the proofs involved, and show that all possible products fall into three interesting and well-characterized families of knots and links. Finally we will mention some important biological applications of our model, including, how it can help determine the sequence of products in multiple rounds of processive recombination, and distinguish between products of processive and distributive recombination.

This is joint work with Dorothy Buck.

timetable:
Wed 15 Jun, 17:45 - 18:30, Aula Dini
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