Abstract
We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution <= 3.0 angstrom. Such contacts may be of either the lone pair-pi (lp-pi) or the OH-pi type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 angstrom for A, G and C, and approximately at 3.1-3.2 angstrom for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-pi interaction as compared to the OH-pi one (3.0 versus 3.5 angstrom). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-pi or the OH-pi type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the O-W atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization ofwater-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.