A combinatorial study of the effects of admitting non-watson-crick base pairings and of base composition on the helix-forming potential of polynucleotides of random sequence

The development of extensive double-helical secondary structure in random polynucleotides depends on the existence of regions of complementary or nearly complementary base sequence. Although the precise structure assumed in solution by a particular polynucleotide is determined by thermodynamic considerations, a purely statistical investigation of the expected extent of complementarity can yield useful general insights. Such probabilistic techniques are applied to a study of the effects of base composition and of different assumed base-pairing schemes on the extent of secondary structural development in random polynucleotides. The results suggest limitations on the possible evolutionary precursors to the extensive and nearly perfect helical structure exhibited by nucleic acids, such as the cloverleaf of tRNA and the flower model of the MS2 coat protein gene.