Detection of informational complementarity in an amino acid sequence

Abstract

THE existence of extensive base-paired secondary structure in a messenger RNA (mRNA) is of considerable importance in the analysis of the evolution and biosynthesis of the protein thus encoded¹. The amino acid sequence encoded by a looped mRNA sequence consists of two halves that are informationally related, but detection of such relationships in naturally occurring amino acid sequences is complicated by the three possibilities in phasing codons in the antiparallel RNA sequences of the loop. The triplet nucleotide codons within such a loop can be mismatched in two ways or can be exactly matched. Mathematical analysis of naturally occurring amino acid sequences to detect regions of possible informational complementarity is considerably simplified if one restricts the search to situations in which codon to codon matching in RNA loops is possible.