Third Codon G + C Periodicity as a Possible Signal for an "Internal" Selective Constraint

Quasi-local analysis methods, such as window Fast Fourier Transform and an information theoretical quantity known as mutual information, have allowed us to gain some further insights on the importance and the contextual dependence of a pattern found in DNA sequences showing a periodicity of three with a G or C base in the third position. We have screened for such a periodicity, in terms of the alternative "strong" (S = C or G) versus "weak" (W = A or T) base, a large sample of DNA coding and non-coding sequences from both prokaryotes and eukaryotes, with the aim of testing whether this pattern could be considered as a significant signal for past or present constraints regarding DNA organization and/or function. This periodicity was indeed found in a number of sequences always associated with open reading frames, generally confined in prokaryotes living in extreme environments or in highly conserved eukaryotic genes. Moreover, codon usage was found to be very similar even in genes coding for very different functions. The data are discussed in view of their possible implications for an adaptive value of such a periodicity, in terms of more accurate translation processing and better overall stability.