Influence of the p-p Interactions on the Hydrogen Bonding Capacity of Stacked DNA/RNA Bases

Pierre Mignon, Stefan Loverix, Jan Steyaert, Paul Geerlings

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216 Citations (Scopus)
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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.
Original languageEnglish
Pages (from-to)1779-1789
Number of pages11
JournalNucleic Acids Research
Issue number6
Publication statusPublished - 2005

Bibliographical note

Nucl. Acids. Res., 33, 1779-1789, 2005


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