Prevalence of syn nucleobases in the active sites of functional RNAs

Abstract

Biological RNAs, like their DNA counterparts, contain helical stretches, which have standard Watson-Crick base pairs in the anti conformation. Most functional RNAs also adopt geometries with far greater complexity such as bulges, loops, and multihelical junctions. Occasionally, nucleobases in these regions populate the syn conformation wherein the base resides close to or over the ribose sugar, which leads to a more compact state. The importance of the syn conformation to RNA function is largely unknown. In this study, we analyze 51 RNAs with tertiary structure, including aptamers, riboswitches, ribozymes, and ribosomal RNAs, for number, location, and properties of syn nucleobases. These RNAs represent the set of nonoverlapping, moderate-to high-resolution structures available at present. We find that syn nucleobases are much more common among purines than pyrimidines, and that they favor C29-endo-like conformations especially among those nucleobases in the intermediate syn conformation. Strikingly, most syn nucleobases participate in tertiary stacking and base-pairing interactions: Inspection of RNA structures revealed that the majority of the syn nucleobases are in regions assigned to function, with many syn nucleobases interacting directly with a ligand or ribozyme active site. These observations suggest that judicious placement of conformationally restricted nucleotides biased into the syn conformation could enhance RNA folding and catalysis. Such changes could also be useful for locking RNAs into functionally competent folds for use in X-ray crystallography and NMR.

The role of RNA conformation in RNA-protein recognition

“…Taken together, we show that RNA sequences which are bound by the RRM domain are enriched for specific dinucleotides possessing unique RNA conformation. While as expected from the chemical nature of RNA nucleotides we noticed a preference for dinucleotides containing G in syn conformation 44,32 and U in C2' endo conformation, we show that the RNA conformations were non-randomly distributed between all G and U containing dinucleotides, possibly providing an additional recognition code for RNA recognition by the RRM protein family.…”

“…44 This is also in agreement with a previous study that showed a preference for purines among syn nucleobases in functional RNAs. 32 We also noticed that the C2' endo conformation, which was most significant in the RRM binding interfaces, was preferably found in U nucleotides (Table S1). It has been previously shown that the C2' endo unusual sugar pucker conformation provides less steric hindrance compared with the more common conformation C3' endo.…”

“…31 The prevalence of syn conformation was also shown in active sites of functional RNA. 32 Further, we demonstrated that nucleotides possessing the rare conformations are preferentially involved in direct interactions between RNA and small ligand. 33 Here we show that rare RNA conformations are also prevalent among nucleotides which bind proteins, specifically via the RRM domain.…”

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

“…A10 is in a syn-conformation with a C2′-endo sugar pucker. It is possible that a correlation of A10 being in the syn-conformation changes the sugar pucker and thereby changes the A10 phosphate (scissile phosphate) to A11 phosphate distance for appropriate self-cleavage (26). This distance is longer than most other phosphate-phosphate distances (6.8 Å).…”

“…A10 may then be acting to aid for in-line nucleophilic attack. Hammerhead, HDV, glmS, and hairpin ribozymes all have nucleotides in syn-conformation at critical positions around their active site structures (26).…”