Journal article
Pathways of DNA unlinking: A story of stepwise simplification.
- Abstract:
- In Escherichia coli DNA replication yields interlinked chromosomes. Controlling topological changes associated with replication and returning the newly replicated chromosomes to an unlinked monomeric state is essential to cell survival. In the absence of the topoisomerase topoIV, the site-specific recombination complex XerCD- dif-FtsK can remove replication links by local reconnection. We previously showed mathematically that there is a unique minimal pathway of unlinking replication links by reconnection while stepwise reducing the topological complexity. However, the possibility that reconnection preserves or increases topological complexity is biologically plausible. In this case, are there other unlinking pathways? Which is the most probable? We consider these questions in an analytical and numerical study of minimal unlinking pathways. We use a Markov Chain Monte Carlo algorithm with Multiple Markov Chain sampling to model local reconnection on 491 different substrate topologies, 166 knots and 325 links, and distinguish between pathways connecting a total of 881 different topologies. We conclude that the minimal pathway of unlinking replication links that was found under more stringent assumptions is the most probable. We also present exact results on unlinking a 6-crossing replication link. These results point to a general process of topology simplification by local reconnection, with applications going beyond DNA.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 2.2MB, Terms of use)
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- Publisher copy:
- 10.1038/s41598-017-12172-2
Authors
- Publisher:
- Nature Research
- Journal:
- Scientific Reports More from this journal
- Volume:
- 7
- Issue:
- 1
- Article number:
- 12420
- Publication date:
- 2017-09-29
- Acceptance date:
- 2017-09-01
- DOI:
- EISSN:
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2045-2322
- Pmid:
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28963549
- Language:
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English
- Keywords:
- Pubs id:
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pubs:732958
- UUID:
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uuid:e6920738-0682-432a-95ac-e745e564b7e7
- Local pid:
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pubs:732958
- Source identifiers:
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732958
- Deposit date:
-
2019-07-03
Terms of use
- Copyright holder:
- Stolz et al
- Copyright date:
- 2017
- Notes:
- © The Author(s) 2017. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
- Licence:
- CC Attribution (CC BY)
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