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

Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Here, we study the frequencies of occurrence of homooligomers flanked by one base, XnUor UXn, 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 VVUXnor UXnVV oligomers (V = A, C, G, T). With very few exceptions, if the VV and Xnare 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 Xnnucleotides 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.

Original languageEnglish
Pages (from-to)21-42
Number of pages22
JournalJournal of Theoretical Biology
Volume149
Issue number1
DOIs
StatePublished - 7 Mar 1991

Fingerprint

Dive into the research topics of 'The ordering of nucleotides in the DNA: Strong pyrimidine-purine patterns near homooligomer tracts'. Together they form a unique fingerprint.

Cite this