PMID:12857958

Citation	Stone, MD, Bryant, Z, Crisona, NJ, Smith, SB, Vologodskii, A, Bustamante, C and Cozzarelli, NR (2003) Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc. Natl. Acad. Sci. U.S.A. 100:8654-9
Abstract	Escherichia coli topoisomerase (Topo) IV is an essential type II 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.
Links	PubMed PMC166367 Online version:10.1073/pnas.1133178100
Keywords	DNA Replication; DNA Topoisomerase IV/metabolism; DNA, Bacterial/chemistry; DNA, Bacterial/metabolism; DNA, Superhelical/chemistry; DNA, Superhelical/metabolism; Escherichia coli/enzymology; Models, Biological; Models, Molecular; Monte Carlo Method; Nucleic Acid Conformation; Stereoisomerism; Thermodynamics
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