Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 '-OH Group of Ribose

Authors: Sponer, J., Zgarbova, M., Jurecka, P., Riley, KE., Sponer, JE., Hobza, P.
Year: 2009


The folded structures of RNA molecules and large ribonucleoprotein particles are stabilized by a wide range of base pairs that actively utilize the 2'-OH groups of ribose for base pairing. Such base pairing does not occur in DNA and is essential for functional RNAs. We report reference quantum chemical calculations of base pairing energies for a representative selection of 25 RNA base pairs utilizing the ribose moiety for base pairing, including structures with amino acceptor interactions. All base pairs are evaluated at the MP2 level with extrapolation to the complete basis set (CBS) of atomic orbitals. CCSD(T) correction terms were obtained for four base pairs. In addition, the base pairing is evaluated using the DFT-SAPT perturbational procedure along with the aug-cc-pVDZ basis set, which allows for the decomposition of the interaction energies into separate, physically meaningful, components. These calculations confirm that, compared to canonical base pairs, many RNA base pairs exhibit a modestly increased role of dispersion attraction compared to canonical base pairs. However, the effect is smaller than one would assume based on assessment of the ratio of HF and correlation components of the interaction energies. Interaction energies are further calculated using the SCS(MI)-MP2 and DFT-D methods. Finally, we estimate the effect of aqueous solvent screening on the base pairing stability using the continuum solvent approach.