Abstract
The global conformation of long RNA molecules containing bulge or internal loop are typically not well characterized by conventional NMR methods that rely on NOE-derived short-range distance restraints and J-coupling derived torsion angle restraints. Recently, residual dipolar couplings (RDCs) that provide long-range angular information are being used for structure determination of bio-molecules including RNAs. In this study, RDCs were used for structural determination of a model RNA including bulge, and the effect of RDCs on the structure determination was analyzed. The global structure of the model RNA was improved by the refinement with RDCs. Furthermore, the local structure of the bulge was significantly improved, despite RDCs in the bulge region were not included in the refinement. Thus, it was clearly shown that the RDC refinement was valuable for the structure determination of RNAs containing bulge or internal loop.
