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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 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

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)

© Organic and Biomolecular Chemistry, 2014, vol. 12, núm. 26, p. 4691-4700

Royal Society of Chemistry (RSC)

Author: Poater i Teixidor, Jordi
Swart, Marcel
Bickelhaupt, Friedrich Matthias
Fonseca Guerra, Célia
Date: 2014 July 14
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
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)
Format: application/pdf
ISSN: 1477-0520 (versió paper)
1477-0539 (versió electrònica)
Document access: http://hdl.handle.net/10256/11458
Language: eng
Publisher: Royal Society of Chemistry (RSC)
Collection: MICINN/PN 2012-2014/CTQ2011-25086
AGAUR/2009-2014/2009 SGR-528
Reproducció digital del document publicat a: http://dx.doi.org/10.1039/c4ob00427b
Articles publicats (D-Q)
Is part of: © Organic and Biomolecular Chemistry, 2014, vol. 12, núm. 26, p. 4691-4700
Rights: Attribution-NonCommercial 3.0 Spain
Rights URI: http://creativecommons.org/licenses/by-nc/3.0/es/
Subject: ADN -- Estructura
DNA structure
Enllaços d’hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
Title: B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
Type: info:eu-repo/semantics/article
Repository: DUGiDocs

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