Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1093/nar/gkw815 http://hdl.handle.net/11449/162166 |
Resumo: | 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 determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles. |
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Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulationIt 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 determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.Thai Ministry of Science and TechnologyBBSRCNational Science FoundationCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)University of Leeds Advanced Research Computing (ARC) unitsN8 consortiumEPSRCStudienstiftung des deutschen VolkesGerman Academic Exchange Service (DAAD)University of LeedsEngineering and Physical Sciences Research CouncilUniv Leeds, Sch Phys & Astron, Woodhouse Lane, Leeds LS2 9JT, W Yorkshire, EnglandKMUTT, Fac Sci, Theoret & Computat Sci Ctr TaCS, Sci Lab Bldg,126 Pracha Uthit Rd, Bangkok 10140, ThailandUniv Oxford, Rudolf Peierls Ctr Theoret Phys, Parks Rd, Oxford OX1 3PU, EnglandUC Davis Genome Ctr, Hlth Sci Dr, Davis, CA 95616 USASao Paulo State Univ, Dept Phys, Rua Cristovao, BR-15054000 Sao Jose Do Rio Preto, SP, BrazilUniv York, Dept Phys, Biol Phys Sci Inst, York YO10 5DD, N Yorkshire, EnglandUniv Nottingham, Sch Pharm, Univ Pk, Nottingham NG7 2RD, EnglandUniv Nottingham, Ctr Biomol Sci, Univ Pk, Nottingham NG7 2RD, EnglandUniv Oxford, Dept Chem, Phys & Theoret Chem Lab, South Parks Rd, Oxford OX1 3QZ, EnglandUniv Leeds, Astbury Ctr Struct & Mol Biol, Woodhouse Lane, Leeds LS2 9JT, W Yorkshire, EnglandSao Paulo State Univ, Dept Phys, Rua Cristovao, BR-15054000 Sao Jose Do Rio Preto, SP, BrazilBBSRC: BB/I019472/1National Science Foundation: DBI-0850214National Science Foundation: ACI-1053575EPSRC: EP/N027639/1Engineering and Physical Sciences Research Council: EP/N027639/1Oxford Univ PressUniv LeedsKMUTTUniv OxfordUC Davis Genome CtrUniversidade Estadual Paulista (Unesp)Univ YorkUniv NottinghamSutthibutpong, ThanaMatek, ChristianBenham, CraigSlade, Gabriel G. [UNESP]Noy, AgnesLaughton, CharlesDoye, Jonathan P. K.Louis, Ard A.Harris, Sarah A.2018-11-26T17:10:39Z2018-11-26T17:10:39Z2016-11-02info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article9121-9130application/pdfhttp://dx.doi.org/10.1093/nar/gkw815Nucleic Acids Research. Oxford: Oxford Univ Press, v. 44, n. 19, p. 9121-9130, 2016.0305-1048http://hdl.handle.net/11449/16216610.1093/nar/gkw815WOS:000388016900013WOS000388016900013.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengNucleic Acids Research9,025info:eu-repo/semantics/openAccess2023-10-01T06:06:26Zoai:repositorio.unesp.br:11449/162166Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T13:41:14.435965Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
title |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
spellingShingle |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation Sutthibutpong, Thana |
title_short |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
title_full |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
title_fullStr |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
title_full_unstemmed |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
title_sort |
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation |
author |
Sutthibutpong, Thana |
author_facet |
Sutthibutpong, Thana Matek, Christian Benham, Craig Slade, Gabriel G. [UNESP] Noy, Agnes Laughton, Charles Doye, Jonathan P. K. Louis, Ard A. Harris, Sarah A. |
author_role |
author |
author2 |
Matek, Christian Benham, Craig Slade, Gabriel G. [UNESP] Noy, Agnes Laughton, Charles Doye, Jonathan P. K. Louis, Ard A. Harris, Sarah A. |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Univ Leeds KMUTT Univ Oxford UC Davis Genome Ctr Universidade Estadual Paulista (Unesp) Univ York Univ Nottingham |
dc.contributor.author.fl_str_mv |
Sutthibutpong, Thana Matek, Christian Benham, Craig Slade, Gabriel G. [UNESP] Noy, Agnes Laughton, Charles Doye, Jonathan P. K. Louis, Ard A. Harris, Sarah A. |
description |
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 determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-11-02 2018-11-26T17:10:39Z 2018-11-26T17:10:39Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1093/nar/gkw815 Nucleic Acids Research. Oxford: Oxford Univ Press, v. 44, n. 19, p. 9121-9130, 2016. 0305-1048 http://hdl.handle.net/11449/162166 10.1093/nar/gkw815 WOS:000388016900013 WOS000388016900013.pdf |
url |
http://dx.doi.org/10.1093/nar/gkw815 http://hdl.handle.net/11449/162166 |
identifier_str_mv |
Nucleic Acids Research. Oxford: Oxford Univ Press, v. 44, n. 19, p. 9121-9130, 2016. 0305-1048 10.1093/nar/gkw815 WOS:000388016900013 WOS000388016900013.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Nucleic Acids Research 9,025 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
9121-9130 application/pdf |
dc.publisher.none.fl_str_mv |
Oxford Univ Press |
publisher.none.fl_str_mv |
Oxford Univ Press |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128264111128576 |