Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-aminoacridine derivatives

Eur J Biochem. 1989 Jun 15;182(2):437-44. doi: 10.1111/j.1432-1033.1989.tb14850.x.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminoacridines*
  • Azides*
  • Base Sequence
  • Bisbenzimidazole / analysis
  • DNA / analysis*
  • DNA Damage
  • DNA Restriction Enzymes
  • Distamycins / analysis
  • Echinomycin / analysis
  • Indoles / analysis
  • Molecular Sequence Data
  • Molecular Structure
  • Plasmids
  • Receptors, Drug / analysis*
  • Receptors, Drug / genetics


  • Aminoacridines
  • Azides
  • Distamycins
  • Indoles
  • Receptors, Drug
  • DAPI
  • Echinomycin
  • 9-(6-(2-diazocyclopentadienylcarbonyloxy)hexylamino)acridine
  • DNA
  • 9-amino-3-azido-7-methoxyacridine
  • DNA Restriction Enzymes
  • Bisbenzimidazole