How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.
Freshly replicated DNA molecules initially form multiply interlinked right-handed catenanes. In bacteria, these catenated molecules become supercoiled by DNA gyrase before they undergo a complete decatenation by topoisomerase IV (Topo IV). Topo IV is also involved in the unknotting of supercoiled DNA molecules. Using Metropolis Monte Carlo simulations, we investigate the shapes of supercoiled DNA molecules that are either knotted or catenated. We are especially interested in understanding how Topo IV can unknot right-handed knots and decatenate right-handed catenanes without acting on right-handed plectonemes in negatively supercoiled DNA molecules. To this end, we investigate how the topological consequences of intersegmental passages depend on the geometry of the DNA-DNA juxtapositions at which these passages occur. We observe that there are interesting differences between the geometries of DNA-DNA juxtapositions in the interwound portions and in the knotted or catenated portions of the studied molecules. In particular, in negatively supercoiled, multiply interlinked, right-handed catenanes, we detect specific regions where DNA segments belonging to two freshly replicated sister DNA molecules form left-handed crossings. We propose that, due to its geometrical preference to act on left-handed crossings, Topo IV can specifically unknot supercoiled DNA, as well as decatenate postreplicative catenanes, without causing their torsional relaxation.
Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA ejrawdon@stthomas.edu.
Eric J
EJ
Rawdon
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Julien
J
Dorier
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.
Dusan
D
Racko
Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
Kenneth C
KC
Millett
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland Andrzej.Stasiak@unil.ch.
Andrzej
A
Stasiak
D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D027101:DNA Topoisomerase IV / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
D004247:DNA; D027101:DNA Topoisomerase IV