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).
Highlights
The shapes of DNA knots formed in vivo or in vitro are tale-tellers both about the mechanism of the DNA topoisomerases [1,2,3] or site-specific DNA recombinases that produced these DNA knots [4,5,6,7,8,9,10] and about specific arrangements of DNA molecules at the moment they were knotted [11,12,13,14]
We propose a general model of knotting arising during replication that involves both the original model and passages occurring between two different sister duplexes that form precatenanes in partially replicated DNA molecules
Using mathematical formalism of knotted -curves, we have fully characterized the mechanism of formation of DNA knots in partially replicated DNA molecules
Summary
The shapes of DNA knots formed in vivo or in vitro are tale-tellers both about the mechanism of the DNA topoisomerases [1,2,3] or site-specific DNA recombinases that produced these DNA knots [4,5,6,7,8,9,10] and about specific arrangements of DNA molecules at the moment they were knotted [11,12,13,14]. Electron microscopy studies showed that depending on the EM preparation method utilised, the partially replicated DNA plasmids can have either a form with freshly replicated sister duplexes winding around each other forming precatenanes or a form without precatenanes [18]. Sogo et al identified that knotting occurs in partially replicated DNA molecules They characterized the types of knots formed in vivo and concluded that the formed knots demonstrate that in vivo freshly replicated portions of partially replicated DNA molecules wind around each other forming precatenanes [14]. We propose a general model of knotting arising during replication that involves both the original model and passages occurring between two different sister duplexes that form precatenanes in partially replicated DNA molecules. The topological consequences of intra- and inter-sister passages are the same
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