THE NON-B-DNA STRUCTURE OF D(CA/TG)N DIFFERS FROM THAT OF Z-DNA

Chemical probing of two predominantly alternating purine-pyrimidine d(CA/TG)(n) repeats led us to propose previously that in supercoiled plasmids these elements adopt a non-B-DNA structure distinct from that of Z-DNA formed by d(CG)(n) sequences. Here, we present further evidence supporting this contention. Reactivity with the conformation-sensitive reagent chloroacetaldehyde, which reacts with unpaired adenines and cytosines, was confined strictly to adenines in the d(CA/TG)(n) repeat. In contrast, only bases outside the d(CG)(n) repeat exhibited chloroacetaldehyde reactivity. Two-dimensional gel analysis of topoisomers containing d(CA/TG)(n) tracts with bases out of strict purine-pyrimidine alternation revealed multiple superhelical-dependent transitions to an alternative left-handed structure. Within individual plasmid molecules, these multiple transitions resulted from the stepwise conversion of contiguous segments of alternating purine-pyrimidine sequence, which are delimited by bases out of alternation, to the full-length alternative conformation. When the left-handed helices increased in length to include more bases out of alternation, the average helical pitch changed substantially to produce a less tightly wound left-handed helix. Overall, these data indicate that d(CA/TG)(n) tracts adopt a left-handed conformation significantly different from that of the canonical Z-DNA structure of d(CG)(n) sequences.