Solution structure of the DNA complexes with an alkyl-linked bis(benzimidazole) compound, 1,4-bis[5-(4-methyl-1-piperazinyl)-2-benzimidazolyl]butane

Solution structures of the 1:1 complexes of an alkyl-linked bis(benzimidazole) compound (4; Figure 1(a)) with the self-complementary DNA duplexes, d(CGCGAATTCGCG)2 and d(CGCAAATTTGCG)2, have been studied by 1H NMR spectroscopy and molecular mechanics calculations. The intermolecular NOE data and the energy-minimized geometries of the 1:1 complexes indicate that 4 binds in the minor groove of the 5'-GAATTCG and 5'-CAAATTT regions of the DNA duplexes.