Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.
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.
Mignon
Pierre
P
Eenheid Algemene Chemie (ALGC), Faculteit Wetenschappen, Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium.
Loverix
Stefan
S
Steyaert
Jan
J
Geerlings
Paul
P
D020029:Base Pairing; D001555:Benzene Derivatives / Q000737:chemistry; D019295:Computational Biology; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015394:Molecular Structure; D012313:RNA / Q000737:chemistry*; D055672:Static Electricity
D001555:Benzene Derivatives; D012313:RNA; D003596:Cytosine; D004247:DNA