Hydrophobic interactions in the major groove can influence DNA local structure.
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.
Jernigan
R L
RL
Laboratory of Mathematical Biology, National Cancer Institute, Bethesda, MD 20892.
Sarai
A
A
Ting
K L
KL
Nussinov
R
R
D001482:Base Composition; D001483:Base Sequence; D004247:DNA; D008745:Methylation; D009690:Nucleic Acid Conformation; D012995:Solubility
D004247:DNA