Discrimination of the length of double-stranded DNA fragments by the bis-intercalating ligand

Bis-intercalator 2 with two acridine moieties separated by a bis(hexamethylene)viologen linker was synthesized and its binding of calf thymus DNA was studied. Bis-intercalator 2 was designed to cover about a 24 Angstrom stretch of double stranded DNA. The binding constant of bis-intercalator 2 for calf thymus DNA was 1.7 x 10(5) M-1 in 10 mM MES, 1 mM EDTA and 0.1 M NaCl (pH 6.25). The two acridine units of 2 stacked with each other in solution and upon its binding the structure of DNA was perturbed considerably. The binding affinities of the bis-intercalator for DNA duplex fragments of different length, d(AT)(n) where n = 3-8, were estimated by its effect on the DNA melting temperature. It was found that d(AT)(5) with a length of 34 Angstrom was stabilized most by 2. By contrast, quinacrine 1 did not show any stabilizing effect on these DNAs. These results suggest that the bis-intercalator was capable of discriminating the length of double-stranded DNA fragments precisely. This ability of 2 may be applied for the precise separation of double-stranded DNA fragments according to their length.