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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Mar 1;91(5):1898–1902. doi: 10.1073/pnas.91.5.1898

The non-B-DNA structure of d(CA/TG)n differs from that of Z-DNA.

M P Kladde 1, Y Kohwi 1, T Kohwi-Shigematsu 1, J Gorski 1
PMCID: PMC43271  PMID: 8127902

Abstract

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 alteration 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.

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Selected References

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