title: Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification.
abstract: Type IIA topoisomerases modify DNA topology by passing one segment of duplex DNA (transfer or T-segment) through a transient double-strand break in a second segment of DNA (gate or G-segment) in an ATP-dependent reaction. Type IIA topoisomerases decatenate, unknot and relax supercoiled DNA to levels below equilibrium, resulting in global topology simplification. The mechanism underlying this non-equilibrium topology simplification remains speculative. The bend angle model postulates that non-equilibrium topology simplification scales with the bend angle imposed on the G-segment DNA by the binding of a type IIA topoisomerase. To test this bend angle model, we used atomic force microscopy and single-molecule Förster resonance energy transfer to measure the extent of bending imposed on DNA by three type IIA topoisomerases that span the range of topology simplification activity. We found that Escherichia coli topoisomerase IV, yeast topoisomerase II and human topoisomerase IIα each bend DNA to a similar degree. These data suggest that DNA bending is not the sole determinant of non-equilibrium topology simplification. Rather, they suggest a fundamental and conserved role for DNA bending in the enzymatic cycle of type IIA topoisomerases.
authors.affiliation: Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Ashley H
authors.initials: AH
authors.lastname: Hardin
authors.forename: Susanta K
authors.initials: SK
authors.lastname: Sarkar
authors.forename: Yeonee
authors.initials: Y
authors.lastname: Seol
authors.forename: Grace F
authors.initials: GF
authors.lastname: Liou
authors.forename: Neil
authors.initials: N
authors.lastname: Osheroff
authors.forename: Keir C
authors.initials: KC
authors.lastname: Neuman
mesh_terms: D000951:Antigens, Neoplasm / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D006801:Humans; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation
chemical_list: D000951:Antigens, Neoplasm; D004268:DNA-Binding Proteins; D004247:DNA; D004250:DNA Topoisomerases, Type II