title: Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation.
abstract: Due to the helical structure of DNA the process of DNA replication is topologically complex. Freshly replicated DNA molecules are catenated with each other and are frequently knotted. For proper functioning of DNA it is necessary to remove all of these entanglements. This is done by DNA topoisomerases that pass DNA segments through each other. However, it has been a riddle how DNA topoisomerases select the sites of their action. In highly crowded DNA in living cells random passages between contacting segments would only increase the extent of entanglement. Using molecular dynamics simulations we observed that in actively supercoiled DNA molecules the entanglements resulting from DNA knotting or catenation spontaneously approach sites of nicks and gaps in the DNA. Type I topoisomerases, that preferentially act at sites of nick and gaps, are thus naturally provided with DNA-DNA juxtapositions where a passage results in an error-free DNA unknotting or DNA decatenation.
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia.
authors.forename: Dusan
authors.initials: D
authors.lastname: Racko
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Benedetti
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Dorier
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland.
authors.forename: Yannis
authors.initials: Y
authors.lastname: Burnier
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Andrzej.Stasiak@unil.ch.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D004247:DNA / Q000737:chemistry; D004261:DNA Replication; D004264:DNA Topoisomerases, Type I / Q000378:metabolism; D043864:DNA, Catenated / Q000737:chemistry* / Q000378:metabolism; D004270:DNA, Circular / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation
chemical_list: D043864:DNA, Catenated; D004270:DNA, Circular; D004278:DNA, Superhelical; D004247:DNA; D004264:DNA Topoisomerases, Type I