Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by θ-curve analysis.

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Version: Final published version
Serval ID
serval:BIB_A21115AE0E58
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by θ-curve analysis.
Journal
Nucleic acids research
Author(s)
O'Donnol D., Stasiak A., Buck D.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
28/09/2018
Peer-reviewed
Oui
Volume
46
Number
17
Pages
9181-9188
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
Publication Status: ppublish
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).
Keywords
DNA Replication/physiology, DNA Topoisomerase IV/metabolism, DNA, Bacterial/chemistry, DNA, Bacterial/genetics, DNA, Bacterial/metabolism, DNA, Circular/chemistry, DNA, Circular/genetics, DNA, Circular/metabolism, DNA, Superhelical/chemistry, DNA, Superhelical/genetics, Escherichia coli/genetics, Nucleic Acid Conformation, Replication Origin/genetics, Stereoisomerism
Pubmed
Web of science
Open Access
Yes
Create date
20/07/2018 15:20
Last modification date
20/08/2019 15:08
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