Self complementarity in messenger RNA of collagen. I. Possible hairpin structures in regions coding for oligopeptides of glycine, proline (hydroxyproline) and alanine

Abstract

The periodic protein collagen is of special interest for the study of the relationship which exists between the structure of a protein and that of its mRNA, because oligopeptides containing glycine, proline (hydroxyproline) and alanine occur with great frequency in it. Collagen is particularly rich in these amino acids, which have codons containing only G and/or C in the obligatory first and second positions. If unlimited choice of codons for all amino acids were to occur, the stretch of mRNA coding for an alpha-chain should contain about 40% G and 31% C (Bachra et al., 1974). These high values suggest that a considerable degree of secondary structure will occur, unless selective codon use would result in the avoidance of G and C in optional third codon positions. In the present paper putative secondary structure formation in collagen mRNA was studied. This was done by studying the positions and frequencies of hairpin structures which could contain stem sections composed of the coding triplets of the above mentioned amino acids and hairpin sections of 4-40 bases. Calculation of the free energy contributions of such hairpin structures, using published values for the contributions of base-pair stacking, hairpin, bulge and interior loops and also taking into account the possible minimum number of base-pairs required for helix nucleation from a single-strand RNA (3 adjacent AU-pairs or 1 or 2 adjacent GC-pairs) led to the following conclusions. A considerable number of alternative, mutually exclusive hairpins can be constructed.