Hydrophobic interactions in the major groove can influence dna local structure

Robert L. Jemigan, Akinori Sarai, Kai Li Ting, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

Abstract

We have considered hydrophobic interactions among aliphatic hydrocarbon groups in A/T sequences. The slightly overwound sequences (T)“* (A)” yield structures with tightly stacked methyl groups along one side of the major groove. The sequence TTAA may yield a sharp bend by folding together the two pairs of stacked methyls on the opposite sides of the major groove. Thus the sequence can affect the formation of either a smooth bend or a sharp kink. These sequence dependent local conformations may be related to a number of biological results.41

Original languageEnglish
Pages (from-to)41-47
Number of pages7
JournalJournal of Biomolecular Structure and Dynamics
Volume4
Issue number1
DOIs
StatePublished - Aug 1986

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