title: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2'-OH Group of Ribose.
abstract: 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.
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Šponer
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Marie
authors.initials: M
authors.lastname: Zgarbová
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Jurečka
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Kevin E
authors.initials: KE
authors.lastname: Riley
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Judit E
authors.initials: JE
authors.lastname: Šponer
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Hobza