Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases - art. no. 031909

The enzymes that pass DNA through DNA so as to remove entanglements, adenos ine-triphosphate hydrolyzing type-II topoisomerases, are able to suppress t he probability of self-entanglements (knots) and mutual entanglements (link s) between similar to 10 kb plasmids, well below the levels expected, given the assumption that the topoisomerases pass DNA segments at random by ther mal motion. This implies that a 10-nm type-II topoisomerase can somehow sen se the topology of a large DNA. We previously introduced a "kinetic proof-r eading" model which supposes the enzyme to require two successive collision s in order to allow exchange of DNA segments, and we showed how it could qu antitatively explain the reduction in knotting and linking complexity. Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed exper imentally.