Journal of Molecular Evolution

, Volume 63, Issue 3, pp 393-400

First online:

Specific Selection Pressure at the Third Codon Positions: Contribution to 10- to 11-Base Periodicity in Prokaryotic Genomes

  • Amir B. CohanimAffiliated withDepartment of Biotechnology and Food Engineering
  • , Edward N. TrifonovAffiliated withGenome Diversity Center, Institute of Evolution, University of Haifa
  • , Yechezkel KashiAffiliated withDepartment of Biotechnology and Food Engineering Email author 

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Prokaryotic sequences are responsible for more than just protein coding. There are two 10- to 11-base periodical patterns superimposed on the protein coding message within the same sequence. Positional auto- and cross-correlation analysis of the sequences shows that these two patterns are a short-range counter-phase oscillation of AA and TT dinucleotides and a medium-range in-phase oscillation of the same dinucleotides, spanning distances of up to ∼30 and ∼100 bases, respectively. The short-range oscillation is encoded by the amino acid sequences themselves, apparently, due to the presence of amphipathic α-helices in the proteins. The medium-range oscillation, related to DNA folding in the cell, is created largely by a special choice of the bases in the third positions of the codons. Interestingly, the amino acid sequences do contribute to that signal as well. That is, the very amino acid sequences are, to some extent, degenerate to serve the same oscillating pattern that is associated with the degenerate third codon positions.


Prokaryotic genomes DNA periodicity Dinucleotides Codon bias Codon usage Third codon positions Supercoiling