Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

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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

Notes:

DA - 20050324
IS - 1362-4962 (Electronic)
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
RN - 0 (Benzene Derivatives)
RN - 63231-63-0 (RNA)
RN - 71-30-7 (Cytosine)
RN - 9007-49-2 (DNA)
SB - IM