Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-aminoacridine derivatives.
It is demonstrated that DNA photofootprinting analysis of the intercalating depsipeptide echinomycin, and the minor groove-binders distamicyn, 4',6-diamidino-2-phenylindole (DAPI) and Hoechst 33258 can be performed using 9-[6-(2-diazocyclopentadienylcarbonyloxy)hexylamino]acridine (DHA) [Nielsen et al. (1988) Nucleic Acids Res. 16, 3877-3888] or 2-methoxy-6-azido-9-aminoacridine (MAA) [Jeppesen et al. (1988) Nucleic Acids Res. 16, 5755-5770]. Both the extent of the drug-binding sites and their relative strength can be determined with either reagent. DNA has the advantage of giving virtually sequence-uniform DNA photocleavage. On the other hand, structural changes in the DNA are detected by MAA. Using the 232-base-pair EcoRI-PvuII pUC19 restriction fragment, it is found that cleavage protection by distamycin, DAPI and Hoechst 33258 all require an (A.T)4 sequence, whereas protection by echinomycin was confined to a G + C-rich 8-base-pair region.
Jeppesen
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Department of Biochemistry B, Panum Institute, University of Copenhagen, Denmark.
Nielsen
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PE
D000609:Aminoacridines; D001386:Azides; D001483:Base Sequence; D006690:Bisbenzimidazole / Q000032:analysis; D004247:DNA / Q000032:analysis*; D004249:DNA Damage; D004262:DNA Restriction Enzymes; D004214:Distamycins / Q000032:analysis; D004448:Echinomycin / Q000032:analysis; D007211:Indoles / Q000032:analysis; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010957:Plasmids; D011955:Receptors, Drug / Q000032:analysis* / Q000235:genetics
D000609:Aminoacridines; D001386:Azides; D004214:Distamycins; D007211:Indoles; D011955:Receptors, Drug; C007293:DAPI; D004448:Echinomycin; C056129:9-(6-(2-diazocyclopentadienylcarbonyloxy)hexylamino)acridine; D004247:DNA; C044658:9-amino-3-azido-7-methoxyacridine; D004262:DNA Restriction Enzymes; D006690:Bisbenzimidazole