A Bis(guanidinium)alcohol Attached to Hairpin Polyamides: Synthesis, DNA Binding and Plasmid Cleavage.

Bis(guanidinium)alcohols have been designed to react with phosphodiester substrates in a fast transphosphorylation step, a quasi-intramolecular process taking place in contact ion pairs. Here the attachment of such compounds to Dervan-type hairpin polyamides is described. The resulting conjugate1 binds to AT-rich DNA duplexes with affinity similar to that of the parent polyamide as shown by UV melting experiments and CD titrations. Conjugate1 nicks plasmid DNA at concentrations ranging from micromolar to high nanomolar.