2000 , Volume 5, Special issue, p.57-63

Synonymous codons are used for coding amino acids with unequal frequencies. The differences are revealed through comparing groups of genes belonging to different species and different gene groups within one species and analyzing synonymous codon frequencies depending on the codon position in the reading frame. Undoubtedly, the synonymous codon usage complies with certain selective limitations, manifesting themselves at various organization levels within the organism. The goal of this work was to analyze theoretically the patterns of evolutionary drift of synonymous codons formed under the effect of the template mechanism of the protein synthesis, common for all organisms studied. For this purpose, a mathematical model describing the most general properties of the translation machinery structure is developed. Computer-assisted analysis performed suggests that the template principle of translation must have made the evolutionary marks at the level of the frequency pattern of synonymous codon usage taking into account their positions in mRNA. The results obtained are confirmed by experimental data.