Highly Cooperative DNA Dialkylation by the Homodimer of Imidazole−Pyrrole Diamide−CPI Conjugate with Vinyl Linker

Abstract

We synthesized new type of diamide−CPI conjugate possessing a vinyl linker, 7. Sequence-selective alkylation of double-stranded DNA by 7 was investigated by high-resolution denaturing gel electrophoresis using ∼400 bp DNA fragments. Highly efficient alkylation predominantly occurs simultaneously at the purines of 5‘-PyG(A/T)CPu-3‘ site on both strands at a nanomolar concentration of 7. These results suggest that the homodimer of conjugate 7 dialkylates both strands according to Dervan's pairing rule together with a new mode of recognition in which the Im-vinyl linker (L) pair targets G/C base pairs. In addition to the major dialkylation sites, a minor alkylation site was also observed at 5‘-GT(A/T)GC-3‘. This alkylation can be explained by an analogous slipped homodimer recognition mode in which the L−L pair recognizes the A/T base pair. Efficient dialkylation by the homodimer of 7 was further confirmed using oligonucleotides (ODNs). HPLC analysis revealed that the conjugate 7 simultaneously alkylates GN3/AN3 of the target sequences on both strands of ODNs.