DNA tracts composed of only two bases concentrate in gene promoters

We have previously shown that long DNA tracts composed of only two of the bases (“binary DNA”) are highly overrepresented in sequenced eukaryotic genomes. Here we examine gene promoter regions, by superposing all genes in a chromosome at their transcription start sites. We find that of the four motifs made of two bases, three are concentrated in gene promoters: Purine/pyrimidine tracts are highly overrepresented in the promoters of yeast chromosome IV, in Caenorhabditis elegans chromosome I, in Arabidopsis thaliana chromosome 2, and in human chromosomes 14, 21, and 22 (a subset). AT-rich tracts (W tracts) are enriched in the same chromosomes, as well as in Drosophila melanogaster chromosome 2R and in an archeon, M. jannaschii. A third motif, K.M tracts, shows some concentration in D. melanogaster promoters. A propensity of binary DNA to unwind is proposed to explain the high presence of the two-base motifs in gene promoters.