The B-Z transition in supercoiled DNA depends on sequence beyond nearest-neighbors

In order to examine sequence-dependent structural effects in DNA, the ability of alternating purine-pyrimidine fragments to undergo a B-Z transition when cloned in a supercoiled plasmid was determined solely as a function of sequence, with base and nearest-neighbor composition held constant. Sequences of 22 GC and 2 AT base pairs were synthesized such that the AT base pairs varied between contiguous placement and separation by eight GC base pairs. Results show, surprisingly, that the ease of the B-Z transition varies with the position of the two AT base pairs, occurring at lower superhelical densities when AT base pairs are contiguous, and at higher torsional strain when the AT base pairs are moved further apart.