title: Unlinking of supercoiled DNA catenanes by type IIA topoisomerases.
abstract: It was found recently that DNA catenanes, formed during replication of circular plasmids, become positively (+) supercoiled, and the unlinking of such catenanes by type IIA topoisomerases proceeds much more efficiently than the unlinking of negatively (-) supercoiled catenanes. In an attempt to explain this striking finding we studied, by computer simulation, conformational properties of supercoiled DNA catenanes. Although the simulation showed that conformational properties of (+) and (-) supercoiled replication catenanes are very different, these properties per se do not give any advantage to (+) supercoiled over (-) supercoiled DNA catenanes for unlinking. An advantage became evident, however, when we took into account the established features of the enzymatic reaction catalyzed by the topoisomerases. The enzymes create a sharp DNA bend in the first bound DNA segment and allow for the transport of the second segment only from inside the bend to its outside. We showed that in (-) supercoiled DNA catenanes this protein-bound bent segment becomes nearly inaccessible for segments of the other linked DNA molecule, inhibiting the unlinking.
authors.affiliation: Department of Chemistry, New York University, New York, New York, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Vologodskii
mesh_terms: D000951:Antigens, Neoplasm / Q000378:metabolism*; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D000951:Antigens, Neoplasm; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D004250:DNA Topoisomerases, Type II