Chemical and structural characterization of the interaction of bleomycin A₂ with d(CGCGAATTCGCG)₂. Efficient, double-strand DNA cleavage accessible without structural reorganization

A detailed description of the interaction between Fe(II)·bleomycin A₂ and the Dickerson-Drew dodecamer d(CGCGAATTCGCG)₂ is presented. The reaction between bleomycin and this substrate leads to DNA cleavage at two major sites, adenosines and cytidine₁₁, and two minor sites, cytidine₃ and thymidines₈. The pattern and relative intensities of cleavage at these sites was not entirely consistent with what would be predicted based on the preference of the drug for cleavage at the pyrimidines of 5′-GC-3′ and 5′-GT-3′ sites. Insight into the origins of the apparent alteration of selectivity was provided by examination of the structure of the duplex which had been determined by X-ray crystallography. This indicated that the C4′ hydrogens of the two nucleotides located at the strongest cleavage sites, C₁₁ on one strand and A₅ on the other, were oriented toward each other in the minor groove. Two-dimensional NMR measurements and molecular dynamics modeling indicated that a metalloBLM could bind to the duplex in an orientation that positioned the metal center roughly equally close to each of these hydrogen atoms. On the basis of this observation, it was proposed that these two residues represented a double-stranded BLM cleavage site. This hypothesis was tested through the study of the BLM-mediated cleavage of the related decamer duplex, d(CGCGAATTCG)·d(CGAATTCGCG), as well as the hairpin sequence d(CGCGAATTCGIIIITTTTCCCCCGAATTCGCG). By the use of the hairpin oligonucleotide ³²P-labeled alternately at the 5′ and 3′-ends, unequivocal evidence was obtained for BLM-mediated double-strand cleavage. Quantitative analysis of the proportion of damage involving double-strand cleavage was effected by the use of the hairpin substrate; for damage initiated at the predominant cleavage site (cytidine₃₁, analogous to cytidine₁₁ in the dodecanucleotide), it is estimated that 43% of all damage leads to double-stranded lesions. The exceptional efficiency of double-strand cleavage observed in this system must reflect the spatial proximity and orientation of the two sugar H's whose abstraction is required to produce double-stranded lesions.