The interpretation of oligonucleotide maps. A theoretical study of nucleic acid digests with special reference to repeated diverged sequences

Oligonucleotide mixtures produced by the digestion of RNA by specific nucleases can be defined in terms of isostichs (sets of common chain length), compositional isomers, and sequence isomers. Equations are derived to express the distribution of radioactivity on the isostich length, the distribution of compositional isomers on the isostich length, and the distribution of compositional isomers on the proportion of total radioactivity (“intensity”). It is shown how the properties of a “fingerprint” may be calculated from first principles, and conversely how the complexity of a sequence may be estimated from its fingerprint. The equations are tested by means of computer simulations of RNA digestions and their range of applicability is determined. The three distributions are used to analyze the digests of repetitious sequences. It is shown how the parameters of a diverged sequence family can, in a favorable case, be deduced from its fingerprint.