B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation

We have computationally investigated the structure and stability of B-DNA. To this end, we have analyzed the bonding in a series of 47 stacks consisting of two base pairs, in which the base pairs cover the full range of natural Watson-Crick pairs, mismatched pairs, and artificial DNA base pairs. Our...

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Detalles Bibliográficos
Autores: Poater i Teixidor, Jordi, Swart, Marcel, Bickelhaupt, F. Matthias, Fonseca Guerra, Célia
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10256/11458
Acceso en línea:http://hdl.handle.net/10256/11458
Access Level:acceso abierto
Palabra clave:ADN -- Estructura
DNA structure
Enllaços d'hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
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spelling B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvationPoater i Teixidor, JordiSwart, MarcelBickelhaupt, F. MatthiasFonseca Guerra, CéliaADN -- EstructuraDNA structureEnllaços d'hidrogenHydrogen bondingFuncional de densitat, Teoria delDensity functionalsWe have computationally investigated the structure and stability of B-DNA. To this end, we have analyzed the bonding in a series of 47 stacks consisting of two base pairs, in which the base pairs cover the full range of natural Watson-Crick pairs, mismatched pairs, and artificial DNA base pairs. Our analyses provide detailed insight into the role and relative importance of the various types of interactions, such as, hydrogen bonding, π-π stacking interactions, and solvation/desolvation. Furthermore, we have analyzed the functionality of the twist-angle on the stability of the structure. Interestingly, we can show that all stacked base pairs benefit from a stabilization by 6 to 12 kcal mol-1 if stacked base pairs are twisted from 0° to 36°, that is, if they are mutually rotated from a congruent superposition to the mutually twisted stacking configuration that occurs in B-DNA. This holds especially for stacked AT pairs but also for other stacked base pairs, including GC. The electronic mechanism behind this preference for a twisted arrangement depends on the base pairs involved. We also show that so-called "diagonal interactions" (or cross terms) in the stacked base pairs are crucial for understanding the stability of B-DNA, in particular, in GC-rich sequencesWe thank the following organizations for financial support: the HPC-Europa2 Transnational Access program of the European Union, the Netherlands Organization for Scientific Research (NWO), the Ministerio de Ciencia e Innovacion (MICINN, project number CTQ2011-25086), the DIUE of the Generalitat de Catalunya (project number 2009SGR528), the Netherlands National Research School Combination - Catalysis (NRSC-C), and the European Fund for Regional Development (FEDER, grant UNGI08-4E-003)Royal Society of Chemistry (RSC)Ministerio de Ciencia e Innovación (Espanya)Generalitat de Catalunya. Agència de Gestió d'Ajuts Universitaris i de Recerca2014info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10256/11458http://hdl.handle.net/10256/11458© Organic and Biomolecular Chemistry, 2014, vol. 12, núm. 26, p. 4691-4700Articles publicats (D-Q)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)Inglésinfo:eu-repo/semantics/altIdentifier/doi/10.1039/c4ob00427binfo:eu-repo/semantics/altIdentifier/issn/1477-0520info:eu-repo/semantics/altIdentifier/eissn/1477-0539info:eu-repo/grantAgreement/MICINN//CTQ2011-25086AGAUR/2009-2014/2009 SGR-528Attribution-NonCommercial 3.0 Spainhttp://creativecommons.org/licenses/by-nc/3.0/es/info:eu-repo/semantics/openAccessoai:recercat.cat:10256/114582026-05-29T05:05:01Z
dc.title.none.fl_str_mv B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
title B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
spellingShingle B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
Poater i Teixidor, Jordi
ADN -- Estructura
DNA structure
Enllaços d'hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
title_short B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
title_full B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
title_fullStr B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
title_full_unstemmed B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
title_sort B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
dc.creator.none.fl_str_mv Poater i Teixidor, Jordi
Swart, Marcel
Bickelhaupt, F. Matthias
Fonseca Guerra, Célia
author Poater i Teixidor, Jordi
author_facet Poater i Teixidor, Jordi
Swart, Marcel
Bickelhaupt, F. Matthias
Fonseca Guerra, Célia
author_role author
author2 Swart, Marcel
Bickelhaupt, F. Matthias
Fonseca Guerra, Célia
author2_role author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (Espanya)
Generalitat de Catalunya. Agència de Gestió d'Ajuts Universitaris i de Recerca
dc.subject.none.fl_str_mv ADN -- Estructura
DNA structure
Enllaços d'hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
topic ADN -- Estructura
DNA structure
Enllaços d'hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
description We have computationally investigated the structure and stability of B-DNA. To this end, we have analyzed the bonding in a series of 47 stacks consisting of two base pairs, in which the base pairs cover the full range of natural Watson-Crick pairs, mismatched pairs, and artificial DNA base pairs. Our analyses provide detailed insight into the role and relative importance of the various types of interactions, such as, hydrogen bonding, π-π stacking interactions, and solvation/desolvation. Furthermore, we have analyzed the functionality of the twist-angle on the stability of the structure. Interestingly, we can show that all stacked base pairs benefit from a stabilization by 6 to 12 kcal mol-1 if stacked base pairs are twisted from 0° to 36°, that is, if they are mutually rotated from a congruent superposition to the mutually twisted stacking configuration that occurs in B-DNA. This holds especially for stacked AT pairs but also for other stacked base pairs, including GC. The electronic mechanism behind this preference for a twisted arrangement depends on the base pairs involved. We also show that so-called "diagonal interactions" (or cross terms) in the stacked base pairs are crucial for understanding the stability of B-DNA, in particular, in GC-rich sequences
publishDate 2014
dc.date.none.fl_str_mv 2014
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10256/11458
http://hdl.handle.net/10256/11458
url http://hdl.handle.net/10256/11458
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1039/c4ob00427b
info:eu-repo/semantics/altIdentifier/issn/1477-0520
info:eu-repo/semantics/altIdentifier/eissn/1477-0539
info:eu-repo/grantAgreement/MICINN//CTQ2011-25086
AGAUR/2009-2014/2009 SGR-528
dc.rights.none.fl_str_mv Attribution-NonCommercial 3.0 Spain
http://creativecommons.org/licenses/by-nc/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution-NonCommercial 3.0 Spain
http://creativecommons.org/licenses/by-nc/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Royal Society of Chemistry (RSC)
publisher.none.fl_str_mv Royal Society of Chemistry (RSC)
dc.source.none.fl_str_mv © Organic and Biomolecular Chemistry, 2014, vol. 12, núm. 26, p. 4691-4700
Articles publicats (D-Q)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812455

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