Detection of an unusual distortion in A-tract DNA using KMnO4: effect of temperature and distamycin on the altered conformation

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Abstract
The chemical probes potassium permanganate (KMnO4) and diethylpyrocarbonate (DEPC) can be used to.study the contormational flexibility of short tracts of adenine (A-tracts) present in DNA. With these probes, we demonstrate that a novel distortion is induced in a 5 base pair A-tract at low temperature. Formation of this distorted A-tract structure, which occurs in a DNA fragment from the promoter region of the plasmid pBR322, is distinguished by a dramatic increase in the KMnO4 reactivity of the central thymines in this tract at 12°C. This alteration occurs in the absence of any detectable rearrangement in the conformation of the adenines in the complementary strand. Induction of this low temperature A-tract structure is blocked by the minor groove binding drug distamycin. Hydroxyl radical footprintlng of distamycin binding to the fragment containing the d(A)5 tract at 12°C suggests that this drug has two different modes of binding to DNA in agreement with recent NMR data. These experiments show that short A-tracts are capable of forming more than one structural variant of B DNA in solution. The possible relationship between the Intrinsic bending of DNA containing short phased A- tracts and the low temperature A-tract conformation is discussed.