Synthesis, DNA binding, and cleavage studies of novel PNA binding cyclen complexes

A novel coumarin-appended PNA binding cyclen derivative ligand, C1, and its copper(II) complex, C2, have been synthesized and characterized. The interaction of these compounds with DNA was systematically investigated by absorption, fluorescence, and viscometric titration, and DNA-melting and gel-electrophoresis experiments. DNA Melting and viscometric titration experiments indicate that the binding mode of C1 is a groove binding, and C2 is a multiple binding mode that involves groove binding and electrostatic binding. From the absorption-titration data, we can state that the primary interaction between CT DNA and the two compounds may be H-bonds between nucleobases. Fluorescence studies indicate that the binding ability of C1 to d(A)(9) is as twice or thrice as that of other oligodeoxynucleotides. Agarose gel-electrophoresis experiments demonstrate that C2 is an excellent chemical nuclease, which can cleave plasmid DNA completely within 24 h.