Are the hydrogen bonds of RNA (A center dot U) stronger than those of DNA (A center dot T)? A quantum mechanics study
The intrinsic stability of Watson-Crick d(A(.)T) and r(A(.)U) hydrogen bonds was analyzed by employing a variety of quantum-mechanical techniques, such as energy calculations, determination of reactivity indexes, and analysis of electron density topology. The analyses were performed not only for equilibrium gas-phase geometries, but also on hundreds of conformations derived from molecular dynamics (MD) and database analysis. None of our results support the idea that r(A(.)U) hydrogen bonds are intrinsically more stable than those of d(A(.)T). Instead, our data are in accordance with the traditional view that the greater stability of RNA relative to DNA is attributable to a variety of effects (e.g., stacking, sugar puckering, solvation) rather than to a significant difference in the hydrogen bonding of DNA and RNA base pairs.