Codon evolution and conservation of the reading phase in genetic code translation.

The description of the optimized evolution of a code based on 4 nucleotides involves a sequential transition of codons, formed firstly by monomers evolving to dimers and then to triplets, in accordance with the progressive increase of the number of amino acids to be coded. The successive increase in the size of these codons during evolution implies changes in the phase reading of the genetic message, which could become chaotic. In order to overcome this constraint, this paper proposes a codon evolution where two things occur simultaneously: codons change in size and there is an alternation of the molecule which holds the information. For example, the nucleotides of the original oligonucleotide are read as monomers when they are translated to an oligopeptide, but further on, this oligopeptide which is read as amino acid dimers, is translated to a nucleotide form (oligonucleotide). Finally, amino acids conforming a peptide are translated from this oligonucleotide, through a reading of triplets. Although plausible, this evolution is a low-probability process due to the fact that it requires a singular sequence of the oligonucleotide and oligopeptide involved. An alternative hypothesis of evolution is also discussed. It proposes that with the exclusion of the establishment of monomer and dimer codons, there is a direct generation of a code of trinucleotides which arises only when a certain number of amino acids has already been generated. Both hypotheses are discussed in terms of the development of a code in which an optimized hardware is maintained through out its evolution.