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 pla smids 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-sensitiv e 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 chloro acetaldehyde reactivity. Two-dimensional gel analysis of topoisomers c ontaining d(CA/TG)(n) tracts with bases out of strict purine-pyrimidin e alternation revealed multiple superhelical-dependent transitions to an alternative left-handed structure. Within individual plasmid molecu les, these multiple transitions resulted from the stepwise conversion of contiguous segments of alternating purine-pyrimidine sequence, whic h are delimited by bases out of alternation, to the full-length altern ative conformation. When the left-handed helices increased in length t o include more bases out of alternation, the average helical pitch cha nged substantially to produce a less tightly wound left-handed helix. Overall, these data indicate that d(CA/TG)(n) tracts adopt a left-hand ed conformation significantly different from that of the canonical Z-D NA structure of d(CG)(n) sequences.