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.