Sequence dependence of DNA structure. The B, Z, and A conformations of polydeoxynucleotides containing repeating units of 6 to 16 base pairs.

In order to study the sequence dependence of the B-Z transition, we have synthesized eight double-stranded polydeoxynucleotides. The polymers have defined alternating purine-pyrimidine sequences with repeating units of 6-16 base pairs, and contain 12.5-33% AT base pairs. A and T nucleotides are in nearest-neighbor positions in the series poly[d[TA(CG)2-7]], but are isolated from each other, with minimum separations of 2 and 6 GC base pairs, in poly[d[TGCA(CG)6]] and poly[T(GC)3A(CG)4)]], respectively. All of the polymers except poly[d[TA(CG)2]] were shown by circular dichroism to undergo a right- to left-hand helical transition at high NaCl concentrations, and all polymers exhibited a B to A transition in the presence of ethanol. Poly[d[TA(CG)7]] was the only polymer to undergo a B to Z to A transition in ethanol. At a constant percentage of AT base pairs, the B-Z transition is sequence-dependent, occurring at lower salt concentrations for polymers containing longer runs of contiguous GC base pairs in the repeating unit.