A study of the hydrolysis of unfractionated reticulocyte ribosomal ribonucleic acid by pancreatic ribonuclease and its relevance to secondary structure.

1. Unfractionated RNA from reticulocyte ribosomes was hydrolysed with pancreatic ribonuclease at 25 degrees . The molecular weight decreased rapidly to about 3s when about 6% of the residues were soluble in 0.5n-perchloric acid. In the early stages 60-80% of the hydrolysed linkages were ;hidden'. The denaturation spectrum was affected. Continued hydrolysis led to slow changes in S value, in the electrophoresis pattern in polyacrylamide gels and in the denaturation spectrum. 2. Hydrolysis of RNA with alkali to fragments of between 2.8s and 5.9s led to changes in the denaturation spectrum similar to those observed in the early stages of enzymic hydrolysis. 3. A theory was developed to relate changes in secondary structure with main-chain scission. 4. The results agree with the ;hairpin-loop' model for RNA. The denaturation studies are consistent with the presence of more than one species of hairpin loop that differ in their denaturation spectra. The average length of the hairpin loop was estimated to be 10-20 residues and an upper limit of 35 residues was established. 5. It is inferred, on the basis of studies with model compounds, that the stability of single-stranded stacked structures is hardly dependent on salt concentration. 6. The denaturation spectrum of the fragments obtained on hydrolysis became less dependent on ionic strength, suggesting that double-helical structures revert to a single-stranded stacked form on denaturation.