Sequence-Specific Cleavage of DNA by Oligonucleotide-Bound Metal Complexes

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2,6-Dicarboxypyridine (DCP) and N,N-bis(2-picolyl)amine (DPA) ligands were synthesized and attached via ethylene groups to the 5′-ends of 12-base oligonucleotides. The base-sequence of the oligonucleotide probes were chosen to be 5′-T-C-G-C-C-T-T-G-C-A-G-C-3′, which is complementary to a 12-base sequence in pUC9 plasmid DNA. When hybridized to a denatured BamHI/PvuI restriction fragment of pUC9 in the presence of Fe2+, oxygen, and a reducing agent, these probes afforded specific cleavage at their complementary sequences in the 135-base-pair template. Analysis of the cleavage fragments by high-resolution polyacrylamide gel electrophoresis indicated that both probes cleaved DNA at a single stretch of bases near the position of the tethered ligand. The cleaving activity of DPA-12-mer was unusually high and extended over eight contiguous nucleotides. DCP-12-mer showed an unprecedented high cleavage specificity extending over two nucleotides only.