The Classification of Rational Subtangle Replacements, with Applications to Complex Nucleoprotein Assemblies

speaker: Dorothy Buck (Imperial College London)

abstract: Many proteins cleave and reseal DNA molecules in precisely orchestrated ways. Modelling these reactions has often relied on the axis of the DNA double helix being circular, so these cut-and-seal mechanisms can be tracked by corresponding changes in the knot type of the DNA axis. However, when the DNA molecule is linear, or the protein action does not manifest itself as a change in knot type, or the knots types are not 4-plats, these knot theoretic models are less germane.

We thus give a taxonomy of local DNA axis configurations. More precisely, we characterise all rational tangles obtained from a given rational tangle via a rational subtangle replacement (RSR).

Biologically then, this classification is endowed with a distance that determines how many enzyme-mediated reactions of a particular type are needed to proceed from one local DNA conformation to another, or indeed if it is even possible.

We conclude by discussing a variety of biological applications of this categorisation, including type-II topoisomerase, site- specific recombinase, and transposase-mediated reactions.

This is joint work with Ken Baker.

timetable:
Wed 15 Jun, 9:00 - 10:00, Aula Dini
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