RELEVANCE

In intensively developing synthetic biology, synonymous gene recoding is the leading method, not without failures in its use.

OBJECTIVE

To identify natural limitations in the use of codons in genes.

MATERIALS AND METHODS

The nucleotide composition, the translational code of the proteins encoded by them, the composition of dinucleotides, dicodones and tricodones were studied by computer analysis in 30 genes of viruses, bacteria, archaea and humans. Sequences of quantitative indicators of codons (complementarity indices and dimension indices) were used to identify limitations in gene coding.

RESULTS

Each gene had identified limitations (private) on the nucleotide composition, translational code, the composition of dinucleotides and dicodons. A common limitation in gene coding is that the difference in complementarity indices of adjacent tricodons, read with a shift of the frame by one codon, as it happens when mRNA is translated on ribosomes, is overwhelmingly no more than 2.

CONCLUSION

Since each codon in the genes, with the exception of the first and last three codons, is included in three sequentially read tricodons, the complementarity indice of each codon is associated with complementarity indices of the two preceding and two subsequent codons. This leads to the recognition of the existence of a continuum of codon connectivity in genes by the values of their complementarity indices.