Conserved geometrical base-pairing patterns in RNA

Abstract

1. INTRODUCTION 3992. DEFINITIONS 4013. CIS BASEPAIRS 4103.1 Cis Watson–Crick/Watson–Crick 4103.2 Wobble pairings 4113.3 Cis Watson–Crick/Hoogsteen pairings 4163.4 Bifurcated pairings 4173.5 Cis open and water-inserted 4214. TRANS BASEPAIRS 4234.1 Trans Watson–Crick/Watson–Crick 4234.2 Trans wobble pairs 4244.3 Trans Watson–Crick/Hoogsteen pairs 4244.4 Trans Hoogsteen/Hoogsteen pairs 4304.5 Trans bifurcated pairings 4325. SHALLOW-GROOVE PAIRINGS 4325.1 Hoogsteen/Shallow-groove pairs 4335.2 Watson–Crick/Shallow-groove pairings 4385.3 Shallow-groove/Shallow-groove pairings 4406. SIDE-BY-SIDE BASES 4467. DEFINING A LIBRARY OF ISOSTERIC PAIRINGS 4468. CONCLUSIONS 4519. ACKNOWLEDGEMENTS 45210. REFERENCES 452RNA molecules fold into a bewildering variety of complex 3D structures. Almost every new RNA structure obtained at high resolution reveals new, unanticipated structural motifs, which we are rarely able to predict at the current stage of our theoretical understanding. Even at the most basic level of specific RNA interactions – base-to-base pairing – new interactions continue to be uncovered as new structures appear. Compilations of possible non-canonical base-pairing geometries have been presented in previous reviews and monographs (Saenger, 1984; Tinoco, 1993). In these compilations, the guiding principle applied was the optimization of hydrogen-bonding. All possible pairs with two standard H-bonds were presented and these were organized according to symmetry or base type. However, many of the features of RNA base-pairing interactions that have been revealed by high-resolution crystallographic analysis could not have been anticipated and, therefore were not incorporated into these compilations. These will be described and classified in the present review. A recently presented approach for inferring basepair geometry from patterns of sequence variation (Gautheret & Gutell, 1997) relied on the 1984 compilation of basepairs (Saenger, 1984), and was extended to include all possible single H-bond combinations not subject to steric clashes. Another recent review may be consulted for a discussion of the NMR spectroscopy and thermodynamic effects of non-canonical (‘mismatched’) RNA basepairs on duplex stability (Limmer, 1997).