Solution structures of the DNA complexes with alkyl-linked bis(benzimidazole) compounds studied by NMR spectroscopy

We have synthesized two novel alkyl-linked bis(benzimidazole) compounds related to pentamidine. The solution structures of 1:1 complexes of these compounds with the self-complementary DNA duplexes, d(CGCGAATTCGCG)2 (A2T2) and d(CGCAAATTTGCG)2 (A3T3) have been studied by one- and two-dimensional 1H NMR spectroscopy. The intermolecular NOE data of the A3T3 complexed with compound 3 indicate that 3 binds in the minor groove of the central 5'-CAAATTTG region of A3T3.