A study of the alkaline hydrolysis of fractionated reticulocyte ribosomal ribonucleic acid and its relevance to secondary structure.
1. RNA isolated from the sub-units of rabbit reticulocyte ribosomes was hydrolysed by 0.4n-potassium hydroxide at 20 degrees . The probability of main-chain scission was calculated from the number-average chain length, which was obtained from S(25,w) in 0.01m-phosphate buffer. 2. The fraction, f, of the original secondary structure that the fragments re-formed at neutral pH in 4m-guanidinium chloride, as well as in 0.01m- and 0.1m-phosphate buffer, was derived from changes in extinction over the range 220-310mmu on thermal denaturation. 3. The secondary structure of RNA is regarded as an assembly of hairpin loops each of 2N+b residues on average, where N is the number of base-paired residues and b is the number of unpaired residues. 4. If chain scission takes place at random then 2N+b=logf/log(1-p). 5. For RNA from the smaller sub-unit 2N+b was estimated as 25+/-5 residues, compared with 30+/-5 residues for the less stable species and 35+/-5 residues for the more stable species of hairpin loop of RNA from the larger sub-unit.