Study of a perturbation in the coding periodicity

The statistical study of different populations of genes, with principal component analyses (PCA) and with mean curves, shows: (1) The occurence probability of the dinucleotide D'=RY (D'=YR), R being a purine base, Y a pyrimidine base, and N any base, after the occurence of the nucleotide Y (R) in the zero modulo three curve—in the eukaryotic protein coding genes—presents a modulo 9 periodicity with a maximum value nine bases after Y (R). This modulo 9 periodicity is added to the existing coding modulo 3 periodicity RNY, i.e. to the preferential use of the codon RNY in the open reading frame. (2) The occurrence probability of the trinucleotide T=YRY after the occurrence of the nucleotide Y—in the protein coding genes of eukaryotes, chloroplasts, and mitochondria, and in the transfer RNA genes—presents a maximum value eight bases after Y. (3) Similar results are obtained (with less statistical significance) with other gene taxonomic groups (viral protein coding genes, viral introns) and with the complementary motif R(N)₈RYR. These results may suggest that the motifs Y(N)₈YRY, R(N)₈RYR, Y(N)₉RY, and R(N)₉YR could have a function related to the spatial structure of the DNA sequences.