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Nucleic Acids Research 2005 33(6):1779-1789; doi:10.1093/nar/gki317
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Published online 23 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Influence of the {pi}–{pi} interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

Pierre Mignon1, Stefan Loverix1,2, Jan Steyaert2 and Paul Geerlings1,*

1Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium 2Eenheid van Moleculaire en Cellulaire Interacties, VIB (Vlaams Interuniversitair Instituut Biotechnologie), Faculteit Wetenschappen, Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium

*To whom correspondence should be addressed. Tel: +32 2 629 33 14; Fax: +32 2 629 33 17; Email: pgeerlin{at}vub.ac.be

Received December 21, 2004. Revised February 8, 2005. Accepted March 2, 2005.

The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA–DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.


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