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Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation

Sutthibutpong, Thana; Matek, Matek; Benham, Craig; Slade, Gabriel G.; Noy, Agnes; Laughton, Charles A.; Doye, Jonathan P.K.; Louis, Ard A.; Harris, Sarah A.

Authors

Thana Sutthibutpong

Matek Matek

Craig Benham

Gabriel G. Slade

Agnes Noy

Charles A. Laughton

Jonathan P.K. Doye

Ard A. Louis

Sarah A. Harris



Abstract

It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks deter- mine the levels of transcription of a given gene at a given time. Using three complementary computa- tional techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are con- strained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any require- ment for external signalling factors. Our models com- bine atomistic molecular dynamics (MD) with coarse- grained simulations and statistical mechanical calcu- lations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denatura- tion in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informa- tional transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.

Citation

Sutthibutpong, T., Matek, M., Benham, C., Slade, G. G., Noy, A., Laughton, C. A., …Harris, S. A. (2016). Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Research, 44(19), 9121–9130. https://doi.org/10.1093/nar/gkw815

Journal Article Type Article
Acceptance Date Sep 3, 2016
Online Publication Date Sep 22, 2016
Publication Date Sep 22, 2016
Deposit Date May 19, 2017
Publicly Available Date May 19, 2017
Journal Nucleic Acids Research
Print ISSN 0305-1048
Electronic ISSN 1362-4962
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 44
Issue 19
Article Number gkw815
Pages 9121–9130
DOI https://doi.org/10.1093/nar/gkw815
Public URL http://eprints.nottingham.ac.uk/id/eprint/42944
Publisher URL https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw815
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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