The ordering of nucleotides in the DNA: Strong pyrimidine-purine patterns near homooligomer tracts

Here, we study the frequencies of occurrence of homooligomers flanked by one base, X_nUor UX_n, where X = A, C, G, T and U ≠ X. Specifically, we search for preferences (or discriminations) in their nearest neighbor doublet, VV. Extensive analysis of the data base reveals striking patterns in such VVUX_nor UX_nVV oligomers (V = A, C, G, T). With very few exceptions, if the VV and X_nare composed of complementary nucleotides, those oligomers having a pyrimidine (Y)-purine (R) junction are preferred over those with an RY one. If the VV and X_nnucleotides are not complementary, the RY junction oligomers are preferred over their YR counterparts. These trends are observed consistently in eukaryotic and prokaryotic sequences. They are particularly striking in the YR > RY oligomers containing complementary nucleotides. The general preferences and discriminations described here are in the same direction as our previous results for homooligomer tracts. These recurrences, along with some additional universal "rules", aid in our understanding of the ordering of nucleotides in the DNA.