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

TY - JOUR

T1 - Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-aminoacridine derivatives

AU - Nielsen, Peter E.

PY - 1989/6/15

Y1 - 1989/6/15

N2 - 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.

AB - 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.

KW - Aminoacridines

KW - Azides

KW - Base Sequence

KW - Bisbenzimidazole/analysis

KW - DNA/analysis

KW - DNA Damage

KW - DNA Restriction Enzymes

KW - Distamycins/analysis

KW - Echinomycin/analysis

KW - Indoles/analysis

KW - Molecular Sequence Data

KW - Molecular Structure

KW - Plasmids

KW - Receptors, Drug/analysis

M3 - Journal article

C2 - 2472274

SN - 1742-464X

VL - 182

SP - 437

EP - 444

JO - FEBS Journal

JF - FEBS Journal

IS - 2

ER -