title: Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions.
abstract: Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis and quantum mechanics approach to calculate accurate energies of the most frequent tRNA tertiary base pairing interactions. Our analysis indicates that six out of the nine classical tertiary interactions are held in place mainly by H-bonds between the bases. In the remaining three cases other effects have to be considered. Tertiary base pairing interaction energies range from -8 to -38 kcal/mol in yeast tRNA(Phe) and are estimated to contribute roughly 25% of the overall tRNA base pairing interaction energy. Six analyzed posttranslational chemical modifications were shown to have minor effect on the geometry of the tertiary interactions. Modifications that introduce a positive charge strongly stabilize the corresponding tertiary interactions. Non-additive effects contribute to the stability of base triplets.
authors.affiliation: Centro Linceo Interdisciplinare Beniamino Segre, Accademia dei Lincei, I-00165 Rome, Italy. romina.oliva@uniroma1.it
authors.forename: Romina
authors.initials: R
authors.lastname: Oliva
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003062:Codon; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry*; D012360:RNA, Transfer, Phe / Q000737:chemistry; D017423:Sequence Analysis, RNA
chemical_list: D003062:Codon; D012360:RNA, Transfer, Phe; D012343:RNA, Transfer