NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2:: Probing the structural features that shape the thermodynamic stability of GA Pairs

The NMR structures of (5'GCU (GA) under bar GGCU3')(3'UCGGAGUCG5') and (5'GCG (GA) under bar UGCU3')(3'UCGUAGGCG5') are reported. The internal loop, (5'U (GA) under bar G3')(3'GAGU5')is about 2 kcal/mol more stable than (5'G (GA) under bar U3')(3'UAGG5')at 37 degrees C. The duplexes assemble into similar global folds characterized by the formation of tandem sheared GA pairs. The different stabilities of the loops are accompained by differences in the local structure of the closing GU pairs. In the (5'U (GA) under bar G3')(3'GAGU5'), the GU pairs form a single hydrogen bond involving the amino group, GH22, and the carbonyl group, UO4. This pairing is similar to the GU closing pair of the 690 hairpin loop found in E. coli 16S rRNA. The (5'U (GA) under bar U5')(3'GAGU5') and (5'G (GA) under bar U3')(3'UAGG5') structures reveal how the subtle interplay between stacking and hydrogen bonding determines sequence dependent conformation and thermodynamic stability. Thus, this work provides structural and thermodynamic benchmarks for theoreticians in the ongoing effort to understand the sequence dependence of RNA physicochemical properties.