Title | Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. |
Publication Type | Journal Article |
Year of Publication | 2005 |
Authors | Mignon, P., S. Loverix, J. Steyaert, and P. Geerlings |
Journal | Nucleic Acids Res |
Volume | 33 |
Issue | 6 |
Pagination | 1779-89 |
Date Published | 2005 |
ISSN | 1362-4962 |
Keywords | Base Pairing, Benzene Derivatives, Computational Biology, Cytosine, DNA, Hydrogen Bonding, Models, Chemical, Molecular Structure, RNA, Static Electricity |
Abstract | 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. |
DOI | 10.1093/nar/gki317 |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 15788750 |
PubMed Central ID | PMC1069514 |
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