mRNA periodical infrastructure complementary to the proof-reading site in the ribosome

Virtually all mRNA sequences carry a 3-base periodical pattern, presumably involved in the translation frame monitoring mechanism (Trifonov, E.N., J. Mol. Biol. 194, 643-652, 87). The hidden pattern, 5'-(GHN)n-3' (H representing nonG, N any base), is further refined by extensive computational analysis of mRNA sequences. According to mononucleotide preferences in the three positions of coding triplets, it appears now as 5'-(GHU)n-3'. Dinucleotide frequencies independent of mononucleotides (contrast dinucleotides, 2) generate the motif 5'-(GCU)n-3'. The same motif is found by regarding the expected avoidance of destabilizing base oppositions in hypothetical transient complementary complexes between mRNA and rRNA. This hidden pattern, in its refined consensus form, 5'-(GCU)n-3', is an almost perfect complementary match to a unique site in small subunit rRNA, the universally conserved (3) proofreading loop at position 525 (of E.coli small subunit rRNA): [formula: see text] This strongly suggests that the 525 site is a major structural component of the previously proposed frame-keeping mechanism which is based on the in-frame contacts between mRNA and three segments of rRNA. Consistent with the original proposition, this site is one of three believed to interact with mRNA.