title: Hydrophobic interactions in the major groove can influence DNA local structure.
abstract: We have considered hydrophobic interactions among aliphatic hydrocarbon groups in A/T sequences. The slightly overwound sequences (T)n.(A)n 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.
authors.affiliation: Laboratory of Mathematical Biology, National Cancer Institute, Bethesda, MD 20892.
authors.forename: R L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: A
authors.initials: A
authors.lastname: Sarai
authors.forename: K L
authors.initials: KL
authors.lastname: Ting
authors.forename: R
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA; D008745:Methylation; D009690:Nucleic Acid Conformation; D012995:Solubility
chemical_list: D004247:DNA