Eukaryotic oligomer frequencies are correlated with certain DNA helical parameters

Gregory G. Lennon, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

Abstract

Nucleotide sequences were converted into purine (R)-pyrimidine (Y) series and divided into several groups, embracing higher and lower organisms. The frequencies of R-Y doublets, triplets and quartets in each were calculated. Whereas eukaryotes uniformly show RR + YY > RY + YR, in bacteria and phage no such relationship is observed. The triplet and quartet patterns in higher organisms differ from those seen in prokaryotes. In the higher organisms a correlation is observed between the frequencies of triplets and quartets and some DNA structural parameters. Specifically, the most frequent triplets are those with minimal torsion angle deviations from a regular B-DNA. The most frequent quartets are those with minimal roll angle deviations. No such correlations are observed in prokaryotes. We therefore propose that in eukaryotic DNA, tight, smooth packaging imposes sequence constraints.

Original languageEnglish
Pages (from-to)427-433
Number of pages7
JournalJournal of Theoretical Biology
Volume116
Issue number3
DOIs
StatePublished - 7 Oct 1985

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