Those messages contained in the transcribed DNA are passed to RNA. The transcribed DNA, thus, contains overlapping messages of both DNA and RNA levels. The major mRNA level message is the classical triplet code - RNA-to-protein translation code. The chapters about this code appear in every textbook on molecular biology, and it will not be described here.
Eukaryotic transcripts also carry the RNA splicing code. This code is only poorly described (Breathnach and Chambon, 1981; Mount, 1982), so that existing sequence-based algorithms are not sufficient for detection of the splice sites in the sequences with as high a precision as in natural splicing process.
Overlapping with the protein-coding message, sequence of codons-triplets, is the universal 3-base periodicity with the consensus (G-nonG-N)n (Trifonov, 1987) or, more accurately, (GCU)n (Lagunez-Otero and Trifonov, 1992). Since the mRNA binding sites in the ribosome possess a complementary periodicity (xxC)n, with obligatory cytosines complementary to the frequent guanines of the first codon positions in mRNA, these 3-base periodicities have been interpreted as a device to maintain correct reading frame during translation of mRNA - the framing code (Trifonov, 1987). As described below, the periodical pattern (GCU)n in mRNA appears to be a fossil of very ancient organization of codons (Trifonov and Bettecken, 1997).
The usage of codons corresponding to the same amino acid is known to be different for different organisms and even different genes. Among the alternative codons, the rare codons are of special interest. Their occurrence along the mRNA sequence is not random. It is shown, for example, that clusters of infrequently used codons in prokaryotic mRNA often follow at a distance about 150 triplets from one another. This is interpreted as translation pausing code, to slow down the translation after a protein domain (fold) is synthesized: to give the newly synthesized chain sufficient time for its proper folding (Makhoul and Trifonov, 2002).
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