Specific cleavage of a DNA triple helix by FeII.bleomycin

The specific cleavage of a DNA triple helix by FeII.bleomycin (BLM) is demonstrated. Triplex-specific cleavage was observed on both strands of the 32-base pair (bp) duplex at the duplex-triplex junctions. Strand scission products and alkali labile lesions were both formed. The strongest BLM cleavage site was located at the 5'-duplex-triplex junction, which is also the preferred triplex binding site of intercalating agents [Collier, D. A., Mergny, J.-L., Thuong, N. T., & Hélène, C. (1991) Nucleic Acids Res. 19, 4219-4224]. The preference of BLM for the 5'-junction does not appear to derive from selective intercalative binding at this site. This is supported by the observation that phleomycin, which contains a thiazolinylthiazole moiety rather than a planar bithiazole ring system, exhibited the same selectivity of triplex cleavage as BLM. Cleavage of the triple helix by FeII.BLM was unaffected by concentrations of Mg2+ up to 5 mM, suggesting possible therapeutic applications of this novel DNA target. Molecular-modeling calculations of the triplex region suggested that dramatic variations in minor groove width and depth occur at the duplex-triplex junctions, particularly at the 5'-junction. Moreover, the minor groove at these sites was calculated to be somewhat shallower and wider than the minor groove of B-DNA. These results suggest that the preference of BLM for the duplex-triplex junctions derives from selective recognition of minor groove shape at these sites and thus reflects conformation-selective, rather than sequence-selective, DNA recognition by FeII.BLM.