Synthesis of pyrene—acridine bis-intercalators and effects of binding to DNA

A bis-intercalating compound containing pyrene and 9-aminoacridine chromophores (N-(5-(1-pyrenyl)-pentyl)-6-(9-acridinylamino) hexylamide, I), was prepared and its interaction with double-stranded DNA was investigated. Homologous compounds in which the two chromophores were connected by a linear carbon chain (pentamethylene (II), tetramethylene (III) and methylene (IV)) were also prepared. In acetonitrile solutions of the free ligands, the presence of the proximal pyrene results in reduced acridine fluorescence relative to 9methylaminoacridine (9-MAA), and the degree of quenching increases with decreasing chain length. The quenching process is assigned to exothermic electron transfer from pyrene to the excited 9-aminoacridine (9-AA) chromophore. In the presence of DNA, the relative quenching order is reversed, and I and IV are quenched more strongly than II and III. From linear dichroism experiments, it is concluded that I binds by bis-intercalation of the pyrene and acridine moieties, III and IV undergo intercalation of the acridine chromophore and II binds by partial bis-intercalation at two contiguous sites.