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Knotting dynamics during DNA replication
Author(s) -
Olavarrieta L.,
MartínezRobles M. L.,
Hernández P.,
Krimer D. B.,
Schvartzman J. B.
Publication year - 2002
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1046/j.1365-2958.2002.03217.x
Subject(s) - biology , dna replication , replication (statistics) , dna , plasmid , agarose gel electrophoresis , pre replication complex , dynamics (music) , ter protein , bubble , microbiology and biotechnology , origin of replication , genetics , physics , mechanics , virology , acoustics
Summary The topology of plasmid DNA changes continuously as replication progresses. But the dynamics of the process remains to be fully understood. Knotted bubbles form when topo IV knots the daughter duplexes behind the fork in response to their degree of intertwining. Here, we show that knotted bubbles can form during unimpaired DNA replication, but they become more evident in partially replicated intermediates containing a stalled fork. To learn more about the dynamics of knot formation as replication advances, we used two‐dimensional agarose gel electrophoresis to identify knotted bubbles in partially replicated molecules in which the replication fork stalled at different stages of the process. The number and complexity of knotted bubbles rose as a function of bubble size, suggesting that knotting is affected by both precatenane density and bubble size.