Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases

Escherichia coli topoisomerase (Topo) IV is an essential type 11 Topo that removes DNA entanglements created during DNA replication. Topo IV relaxes (+) supercoils much faster than supercoils, promoting replication while sparing the essential supercoils. Here, we investigate the mechanism underlying this chiral preference. Using DNA binding assays and a single-molecule DNA braiding system, we show that Topo IV recognizes the chiral crossings imposed by the left-handed superhelix of a [+) supercoiled DNA, rather than global topology, twist deformation, or local writhe. Monte Carlo simulations of braid, supercoil, and catenane configurations demonstrate how a preference for a single-crossing geometry during strand passage can allow Topo IV to perform its physiological functions. Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle.