Particular and General Limitations in Gene Coding and Synonymous Recoding of Genes

In the intensively developing field of synthetic biology, synonymous gene recoding is a leading method, which is not without drawbacks in its use. There are natural limitations in the use of codons in genes. Computer analysis in 30 genes of viruses, bacteria, archaea, and human beings was used to study the nucleotide composition, the translational code of the proteins encoded by them, and the composition of dinucleotides, dicodons, and tricodons. To identify limitations in gene coding, sequences of quantitative indicators of codons (complementarity indices (CIs) and dimension indices) were used. For each gene, limitations (particular) in the nucleotide composition, the translational code, and the composition of dinucleotides and dicodons were identified. A general limitation in gene coding is that the difference in the CIs of neighboring tricodons read with a frame shift of one codon, as happens when mRNA is translated on ribosomes, was no more than 2 in the vast majority of tricodons. Since in genes each codon is included in three sequentially read tricodons, with the exception of the first and last three codons, the CI of each codon is associated with the CIs of the two preceding and two subsequent codons. This leads to the recognition of the existence of a continuum of the codon connectivity in genes based on their CI values.