NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling.

RNA NMR is hindered by the large size of most biological RNAs. We present here a simple method for segmental isotopic labeling of an RNA fragment within the context of a larger RNA. The methodology uses transcription and ribozyme cleavage to prepare appropriate ends for RNA ligase catalyzed ligation. We demonstrate that a 64 nucleotide domain of the Hepatitis C virus internal ribosome entry site (IRES) RNA adopts an independently folded domain within the context of the intact, 100 kDa IRES.