In polytene chromosomes of Drosophila hydei and D. melanogaster, Z-DNA was identified in varying distribution after different conditions for fixation were used. When salivary glands were fixed and squashed in 50% acetic acid alone, Z-DNA was found in the less dense DNA regions, such as interbands, some puffs, and a few of the less dense bands. Prefixation that combined ethanol and acetic acid exposure led to prominent immunofluorescent staining of the bands, generally but not strictly correlating with the total DNA content. Separate exposure to ethanol and acetic acid did not cause this band to stain, but if residual ethanol was present after ethanol fixation, subsequent exposure to acid did cause it. Under the more selective acid fixation conditions, Z-DNA reactivity was seen in portions of certain ecdysone-inducible puffs in the induced but not in the resting state; in other inducible regions, the Z-DNA immunoreactivity was not changed on induction. Z-DNA was also identified in polytene chromosomes within isolated nuclei that had been frozen and fixed in ethanol without exposure to acid; this Z-DNA was present in regions of low DNA density.

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