Binding interaction between polycyclic aromatic compounds and DNA by fluorescence displacement method

Noncovalent interaction of polycyclic aromatic compounds (PACs) with DNA is the first step in their DNA-damaging actions. The binding interaction of 15 PACs with DNA was investigated by the fluorescence displacement method. A DNA-binding dye with known binding mode was employed as the fluorescence probe. Addition of a DNA-binding PAC into the dye/DNA conjugate sets up a competition between the probe and the PAC for DNA and results in a reduction in fluorescence signal. When thiazole orange, a DNA intercalator, was employed as the probe, the dissociation constants of 1-hydroxypyrene, 1-aminopyrene, and 1-pyrenebutyric acid with calf thymus DNA were determined to be 0.62, 1.1, and 4.7 microM, respectively. Other PACs, with two to five fused aromatic rings, showed displacement similar to that of 1-pyrenebutyric acid. When the DNA groove-binding agents Hoechst 33258 and 4',6-diamidino-2-phenylindole were used as the probe, none of the PACs exhibited any significant competition with the probe for DNA. The fluorescence data and the viscosity measurement revealed that these PACs interact with DNA predominantly by intercalation instead of the groove-binding mode. The results also suggested that the polar groups on the periphery of the PAC's aromatic ring play a more important role than the number of aromatic rings in determining the binding affinities with DNA. The fluorescence displacement method provides a convenient tool for rapidly investigating the relationship between PAC structure and its DNA-binding properties.