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 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.
Kladde
M P
MP
Department of Biochemistry, University of Wisconsin, Madison 53706.
Kohwi
Y
Y
Kohwi-Shigematsu
T
T
Gorski
J
J
D000079:Acetaldehyde / Q000031:analogs & derivatives; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics; D015180:Electrophoresis, Gel, Two-Dimensional; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics; D011388:Prolactin / Q000235:genetics; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid
D004278:DNA, Superhelical; D009838:Oligodeoxyribonucleotides; D011388:Prolactin; D004247:DNA; C004656:chloroacetaldehyde; D000079:Acetaldehyde