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B-DNA structure and stability: the role of hydrogen bonding, π-π Stacking interactions, twist-angle, and solvation
Poater i Teixidor, Jordi; Swart, Marcel; Bickelhaupt, Friedrich Matthias; Fonseca Guerra, Célia
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)
ADN -- Estructura
DNA structure
Enllaços d'hidrogen
Hydrogen bonding
Funcional de densitat, Teoria del
Density functionals
Attribution-NonCommercial 3.0 Spain
http://creativecommons.org/licenses/by-nc/3.0/es/
Artículo
info:eu-repo/semantics/publishedVersion
Royal Society of Chemistry (RSC)
         

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