Sugar Edge/Sugar Edge Base Pairs in RNA: Stabilities and Structures from Quantum Chemical Calculations

Abstract

Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, the most important tertiary interaction type in functional RNAs. This study provides an in-depth structure and stability analysis for these two base pair families. Gas-phase-optimized geometries are reported for 12 cis and 7 trans SE/SE base pairs and contrasted to their X-ray counterparts. Interaction energies are computed at the RIMP2 level of theory using the density-functional-theory-optimized geometries. There is a good overall agreement between the optimized and X-ray geometries of the cis SE/SE base pairs. In contrast, only three of the seven trans SE/SE binding patterns could be optimized without a significant distortion of the X-ray geometry. Note, however, that many SE/SE base pairs participate in broader networks of interactions; thus it is not surprising to see some of them to deviate from the X-ray geometry in a complete isolation. Computed interaction energies reveal that all 12 known cis SE/SE binding patterns are very stable. Among the trans SE/SE binding patterns, only the rG/rG, rG/rC, and rA/rG base pairs are sufficiently stable in the crystal geometry. Prediction has been made for some structures not yet detected by crystallography, namely, cis rC/rC, rG/rC, rG/rU, and rU/rU and trans rG/rA base pairs. Interestingly, the new cis SE/SE binding patterns are not necessarily isosteric with the remaining 12 members of this family. The trans rG/rA base pair represents a viable option for base pairing in RNA to be identified by future X-ray studies. In a complete lack of structural information, prediction of other unknown members of the trans SE/SE family was not attempted. Analysis of the interaction energies shows a very large electron correlation component of the interaction energy, pointing at the elevated role of dispersion energy as compared to other types of base pairs. This likely is profitable for stabilization of SE/SE binding patterns in polar environments and could be one of the reasons why the A-minor motif is the leading type of tertiary interactions in RNAs.