Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations

Autores
Zeida Camacho, Ari Fernando; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ∼80% of the DNA curvature present in experimentally solved structures. © 2012 American Physical Society.
Fil: Zeida Camacho, Ari Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Pasteur de Montevideo; Uruguay
Fil: Machado, Matías Rodrigo. Instituto Pasteur de Montevideo; Uruguay
Fil: Dans, Pablo Daniel. Instituto Pasteur de Montevideo; Uruguay
Fil: Pantano, Sergio. Instituto Pasteur de Montevideo; Uruguay
Materia
DNA dynamics
Flexibility
Breathing
DNA recognition
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/67809
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/67809
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulationsZeida Camacho, Ari FernandoMachado, Matías RodrigoDans, Pablo DanielPantano, SergioDNA dynamicsFlexibilityBreathingDNA recognitionhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ∼80% of the DNA curvature present in experimentally solved structures. © 2012 American Physical Society.Fil: Zeida Camacho, Ari Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Pasteur de Montevideo; UruguayFil: Machado, Matías Rodrigo. Instituto Pasteur de Montevideo; UruguayFil: Dans, Pablo Daniel. Instituto Pasteur de Montevideo; UruguayFil: Pantano, Sergio. Instituto Pasteur de Montevideo; UruguayAmerican Physical Society2012-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/67809Zeida Camacho, Ari Fernando; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio; Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations; American Physical Society; Physical Review E: Statistical, Nonlinear and Soft Matter Physics; 86; 2; 8-2012; 21903-219101539-3755CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1103/PhysRevE.86.021903info:eu-repo/semantics/altIdentifier/url/https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021903info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-17T10:47:06Zoai:ri.conicet.gov.ar:11336/67809instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-17 10:47:06.544CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
title Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
spellingShingle Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
Zeida Camacho, Ari Fernando
DNA dynamics
Flexibility
Breathing
DNA recognition
title_short Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
title_full Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
title_fullStr Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
title_full_unstemmed Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
title_sort Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
dc.creator.none.fl_str_mv Zeida Camacho, Ari Fernando
Machado, Matías Rodrigo
Dans, Pablo Daniel
Pantano, Sergio
author Zeida Camacho, Ari Fernando
author_facet Zeida Camacho, Ari Fernando
Machado, Matías Rodrigo
Dans, Pablo Daniel
Pantano, Sergio
author_role author
author2 Machado, Matías Rodrigo
Dans, Pablo Daniel
Pantano, Sergio
author2_role author
author
author
dc.subject.none.fl_str_mv DNA dynamics
Flexibility
Breathing
DNA recognition
topic DNA dynamics
Flexibility
Breathing
DNA recognition
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ∼80% of the DNA curvature present in experimentally solved structures. © 2012 American Physical Society.
Fil: Zeida Camacho, Ari Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Pasteur de Montevideo; Uruguay
Fil: Machado, Matías Rodrigo. Instituto Pasteur de Montevideo; Uruguay
Fil: Dans, Pablo Daniel. Instituto Pasteur de Montevideo; Uruguay
Fil: Pantano, Sergio. Instituto Pasteur de Montevideo; Uruguay
description Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ∼80% of the DNA curvature present in experimentally solved structures. © 2012 American Physical Society.
publishDate 2012
dc.date.none.fl_str_mv 2012-08
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/67809
Zeida Camacho, Ari Fernando; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio; Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations; American Physical Society; Physical Review E: Statistical, Nonlinear and Soft Matter Physics; 86; 2; 8-2012; 21903-21910
1539-3755
CONICET Digital
CONICET
url http://hdl.handle.net/11336/67809
identifier_str_mv Zeida Camacho, Ari Fernando; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio; Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations; American Physical Society; Physical Review E: Statistical, Nonlinear and Soft Matter Physics; 86; 2; 8-2012; 21903-21910
1539-3755
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1103/PhysRevE.86.021903
info:eu-repo/semantics/altIdentifier/url/https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021903
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Physical Society
publisher.none.fl_str_mv American Physical Society
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1843606050258812928
score 13.000565

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