Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNAditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)J2. The DNA in the complex with ditercalinium is kinked (by 15') and severely unwound (by 36) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix. and length (7) of the linker. Furthermore, the drug is inactivated when the N-7 position, or to a lesser extent the C-6 position, is substituted with alkyl groups larger than methyl (8), or when the position of the nitrogen at the 7 position within the chromophore is altered (5).To understand the mechanisms ofDNA repair induction by ditercalinium and why minor modifications of the drug result in dramatic changes in activity, we need to establish the details of how the drug interacts with and distorts DNA. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)h2. § A series of NMR studies of DNA-ditercalinium complexes by Roques and coworkers (9-13) has allowed us to compare those results with the x-ray structure described here. The three-dimensional structures of these DNA-drug complexes provide us with the potential to better understand the molecular basis offunction and recognition in DNA repair processes.
MATERIALS AND METHODSThe self-complementary DNA tetramer d(CGCG) was synthesized by the phosphotriester method and purified with Sep-Pak C18 cartridges (Waters). Ditercalinium was kindly supplied by Bernard P. Roques (Paris). Crystals were grown at room temperature in sitting drops by the vapor diffusion method. The crystallization mother liquor initially contained 0.7 mM DNA (single-strand concentration), 16.8 mM sodium cacodylate buffer (pH 6.0), 14 mM ammonium acetate, 0.3 mM spermine tetrahydrochloride, 0.8 mM magnesium chloride, 6% 2-methyl-2,4-pentanediol, and 0.2 mM ditercalinium. The sitting drops were equilibrated against a reservoir of 30% 2-methyl-2,4-pentanediol. Yellow
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