ArticleNucleic acids research2018
Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by θ-curve analysis.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Electrophoretic Mobility Assay to Separate Supercoiled, Catenated, and Knotted DNA Molecules.Bio-protocol · 2024Article
- Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates.Biology · 2021Article
- Topoly: Python package to analyze topology of polymers.Briefings in bioinformatics · 2021Article
- Knot polynomials of open and closed curves.Proceedings. Mathematical, physical, and engineering sciences · 2020Article
- Chromatin Is Frequently Unknotted at the Megabase Scale.Biophysical journal · 2020Article
- Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.Nucleic acids research · 2019Review
- Chromatin Loop Extrusion and Chromatin Unknotting.Polymers · 2018Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During DNA replication in living cells some DNA knots are inadvertently produced by DNA topoisomerases facilitating progression of replication forks. The types of DNA knots formed are conditioned by the 3D organization of replicating DNA molecules. Therefore, by characterizing formed DNA knots it is possible to infer the 3D arrangement of replicating DNA molecules. This topological inference method is highly developed for knotted DNA circles. However, partially replicated DNA molecules have the form of θ-curves. In this article, we use mathematical formalism of θ-curves to characterize the full possibilities of how knotting can occur during replication of DNA molecules in vivo. To do this, we reanalyze earlier experimental studies of knotted, partially replicated DNA molecules and the previously proposed pathway of their formation. We propose a general model of knotting in replication intermediates, and demonstrate that there is an additional, equally important, parallel knotting pathway that also explains how DNA topoisomerases can produce experimentally observed knotted θ-curves. Interestingly, both pathways require intertwining of freshly replicated sister duplexes (precatenanes).
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