B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
dc.contributor.author
dc.date.accessioned
2015-11-09T10:22:58Z
dc.date.available
2015-11-09T10:22:58Z
dc.date.issued
2014-07-14
dc.identifier.issn
1477-0520
dc.identifier.uri
dc.description.abstract
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
dc.description.sponsorship
We 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)
dc.format.mimetype
application/pdf
dc.language.iso
eng
dc.publisher
Royal Society of Chemistry (RSC)
dc.relation
info:eu-repo/grantAgreement/MICINN//CTQ2011-25086/ES/MODELIZACION MULTIESCALAR EN (BIO)QUIMICA/
AGAUR/2009-2014/2009 SGR-528
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Reproducció digital del document publicat a: http://dx.doi.org/10.1039/c4ob00427b
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© Organic and Biomolecular Chemistry, 2014, vol. 12, núm. 26, p. 4691-4700
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Articles publicats (D-Q)
dc.rights
Attribution-NonCommercial 3.0 Spain
dc.rights.uri
dc.subject
dc.title
B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
dc.type
info:eu-repo/semantics/article
dc.rights.accessRights
info:eu-repo/semantics/openAccess
dc.embargo.terms
Cap
dc.type.version
info:eu-repo/semantics/publishedVersion
dc.identifier.doi
dc.identifier.idgrec
020648
dc.contributor.funder
dc.relation.ProjectAcronym
dc.identifier.eissn
1477-0539