Third Codon G + C Periodicity as a Possible Signal for an "Internal"
Selective Constraint
P. Lió, S. Ruffo, M. Buiatti
Journal of Theoretical Biology, 171(2),215-223 (Nov 21, 1994).
Abstract
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.
