Unmasking a hidden DNA-supercoil relaxation activity in a site-specific recombination system

Abstract: The tyrosine superfamily of recombinases generates knotted products when acting on inverted target sites in circular, supercoiled DNA. For the Cre/loxP system prime torus knots are formed exclusively even for strongly supercoiled DNA substrates. This is surprising because models that are used to describe the recombination reaction predict the appearance of complex knot types over the course of repeated reaction cycles due to the release of mechanical energy stored in supercoiled DNA. We solved this puzzle by revealing a hidden DNA-supercoil relaxation activity that accompanies Cre/loxP recombination through a detailed kinetic analysis of the joint distribution of DNA knot type and linking number. A biophysical model for the time evolution of topological states in circular DNA generated by multiple reaction cycles of recombination shows that the time-dependent knot distributions observed in experiments can only be quantitatively explained by a model that includes DNA unwinding. Thus, the detailed dynamics of transitions between topological states in knotted supercoiled DNA unravels an important aspect of the Cre/loxP recombination mechanism that could not be discerned without probing the time dependence of the recombination mechanism.

geometric topology

Audience: researchers in the topic

GEOTOP-A seminar

Series comments: Web-seminar series on Applications of Geometry and Topology