DISTINGUISHING BETWEEN DUPLEX AND HAIRPIN FORMS OF RNA BY N-15-H-1 HETERONUCLEAR NMR

A general method is described for distinguishing RNA hairpins from RNA duplexes by application of two-dimensional filtered nuclear Overhauser enhancement spectra on a 1:1 mixture of unlabeled and 99% N-15-labeled molecules. The method is applied to the RNA dodecamer rGGCGCUUGCGUC which can form an intramolecular hairpin under low salt conditions and a duplex in high salt. This procedure allows unambiguous identification of RNA hairpins or duplexes under the same conditions that are used in the NMR solution structure determination.