Proof of Phosphate Diester Binding Ability of Cytotoxic DNA-Binding Complexes.

We have rationally designed a family of dinuclear transition-metal complexes to bind two neighboring phosphate diester groups of DNA. The two metal ions are positioned at the distance of two neighboring phosphate diesters in DNA of 6-7 Å by a 1,8-naphthalenediol backbone. Two sterically demanding dipicolylamine pendant arms in the 2 and 7 positions stabilize coordination of the metal ions and prevent coordination to the less exposed nucleobases of DNA. Although the dinuclear Ni and Cu bind to DNA, inhibit DNA synthesis, and preferentially kill human cancer cells over fast proliferating human stem cells, the DNA binding mode was elusive. Here, we prove the principle phosphate diester binding ability of this family of dinuclear complexes by a new dinuclear Ni complex with dibenzimidazolamine pendant arms. The distance of the oxygen atoms of the coordinated phosphate diesters of 6.5 Å confirms the initial design and binding ability to two neighboring phosphate diesters of the DNA backbone. Moreover, the facile exchange of coordinated acetates by phosphate diesters indicates a preferential binding to phosphate diesters.