The effect of RNA secondary structure on the action of a nucleolar endoribonuclease

The effect of the folded macromolecular structure of RNA on the action of a purified single strand specific nucleolar ribonuclease was studied by comparing the limited hydrolysis of defined RNA substrates. The nucleolar RNase was shown to attack only single-stranded regions of the native 5.8 S rRNA, consistent with a computer-derived model for the secondary structure (Nazar, R. N., Stitz, T. O., and Busch, H. (1975) J. Biol. Chem. 250, 8591-8597). The single strand specific nucleolar RNase, unlike S1 nuclease, does not release the end-labeled nucleotide and therefore provides a more useful probe for structural analysis at or near 3'- or 5'-terminal ends of an RNA molecule. Although attacking only single strand regions of the native 5.8 S rRNA, the selectivity of the nucleolar RNase, when compared to S1 nuclease, is distinct and supports the suggestion that other factors besides the proposed secondary structure must also influence nuclease attack. The selective and limited attack of the nucleolar RNase on native RNA was similarly observed using mouse 45 S preribosomal RNA as a substrate and possibly suggests a role for this nucleolar RNase in ribosomal RNA processing.