Abstract
Unlike regular double stranded DNAs, which are stabilized through the formation of canonical Watson Crick base pairs, 3D structures of self-folded single stranded RNA molecules utilize a variety of noncanonical base pairs in order to attain their stable native geometry. Understanding the protein-like complex functionality of RNA molecules, at the molecular level, requires detailed studies on the geometries, interaction energies and stabilities of these base pairs in their respective structural and functional context of occurrence. Rapid growth in the number of solved RNA structures, and the availability of algorithms for automated detection and geometric classification of base pairs, have provided us with a challenging opening for quantum chemical inputs in the exciting area of RNA structural biology.[1-8] Here we specifically discuss noncanonical base pairs belonging to the Cis Hoogsteen-sugar edge (H:S) family, also known as the platform family, which play important structural role in folded RNA molecules.[1] We present results of detailed theoretical investigations of these base pairs, which involve sugar-base hydrogen bonding through 2-OH group of ribose. The studied structures were relaxed at the B3LYP/6-31G(d,p) level, and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs were characterized in terms of number and nature of H-bonds, RMSD values observed on optimization, base pair geometrical parameters and sugar pucker analysis. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. Our studies explore these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab-initio computation of interaction energies. In addition, alternative classification of base pairs and triplets, which provides insights into intrinsic properties of these base pairs and their possible structural and functional roles, will be discussed.