ArticleNucleic acids research2016
How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Article
- Article
- Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects.Nucleic acids research · 2024Article
- Electrophoretic Mobility Assay to Separate Supercoiled, Catenated, and Knotted DNA Molecules.Bio-protocol · 2024Article
- Design, Synthesis, Molecular Modeling, Biological Activity, and Mechanism of Action of Novel Amino Acid Derivatives of Norfloxacin.ACS omega · 2023Article
- Knot Formation on DNA Pushed Inside Chiral Nanochannels.Polymers · 2023Article
- The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG.Nucleic acids research · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites.Molecular cell · 2021Article
- Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates.Biology · 2021Article
- Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism ofPharmaceuticals (Basel, Switzerland) · 2021Article
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- What makes a type IIA topoisomerase a gyrase or a Topo IV?Nucleic acids research · 2021Review
- Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.Nucleic acids research · 2019Review
- Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA.Nucleic acids research · 2019Article
- Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking.Nucleic acids research · 2018Article
- Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.Nucleic acids research · 2018Article
- ClinicalFrontiers in microbiology · 2018Article
- The Global Regulatory Cyclic AMP Receptor Protein (CRP) Controls Multifactorial Fluoroquinolone Susceptibility in Salmonella enterica Serovar Typhimurium.Antimicrobial agents and chemotherapy · 2017Article
- Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe.Nucleic acids research · 2017Article
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Authors and funding
5 authors.
Funding
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Abstract
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.
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