Hydrolysis of polynucleotides and the characterization of their secondary structure. A theoretical study

1. Single-stranded RNA may be regarded as an assembly of L hairpin loops each stabilized by N base pairs and each containing b unpaired residues; one loop is connected to another by c residues. 2. A theory based on the statistics of the random degradation of linear polymers was developed to relate N, b and c with the probability, p, of hydrolysing a diesterified phosphate bond. 3. The number of residues per hairpin loop, which is 2N+b, is related to the fraction, f, of the original loops remaining intact by the equation: 2N+b=logf/log(1–p). 4. The theory was extended to show that the number of residues per loop may be evaluated by fractionating the RNA after hydrolysis and examining the secondary structure of each fraction. Fragments that are shorter than the hairpin loop cannot reproduce the original secondary structure. The probability that a fragment will form an intact loop increases most rapidly for fragments of between 2N+b and 2(2N+b)+c residues. 5. The probability of producing a fragment capable of forming one, and only one, hairpin loop was related to N, b and c.