SELF-ASSOCIATION AND DNA-BINDING PROPERTIES OF 2 TRIPLE HELIX-SPECIFIC LIGANDS - COMPARISON OF A BENZO[E]PYRIDOINDOLE AND A BENZO[G]PYRIDOINDOLE

The self-association and DNA-binding properties of two benzopyridoindole derivatives, 3-methoxy-7H-8-methyl-11-[(3'-aminopropyl)amino]benzo[e]pyrido[4,3-b]indole (BePI) and 3-methoxy-7-[((3'-diethylamino)propyl)amino]-10-methyl-11H-benzo[g]pyrido[4,3-b]indole (BgPI), have been investigated by a variety of NMR, spectrophotometric, fluorescence, and hydrodynamic techniques. NMR studies indicate that both BePI and BgPI self-associate in solution, probably forming multimers (n-mers) in the process. BgPI self-associates with a 3-fold (at 80-degrees-C) to 12-fold (at 27-degrees-C) higher affinity than BcPI. Self-association interactions do not interfere with those between either ligand and DNA at total ligand concentrations less-than-or-equal-to 10(-5) M. Thermodynamic (van't Hoff) analyses of the self-association interactions of both ligands indicate that they are enthalpically driven, consistent with those of other aromatic dyes. Furthermore, at temperatures ranging from 22 to 80-degrees-C, BgPI self-associated complexes are 1.2-1.5 kcal/mol more stable than the corresponding BePI self-associated complexes. The solvent exchange properties of the exchangeable protons of both BePI and BgPI, as determined by NMR studies in H2O at [multimer]/[monomer] ratios of almost-equal-to 4, reveal exchange in the following order as a function of either pH or temperature: 10-NH > 11-NH >> 7-NH >> 3'-NH for BePI and 8-NH > 7-NH >> 11-NH >> 3'-NH for BgPI (see Figure 1 for numbering systems of atoms). These studies also suggest that stacking interactions between heterocyclic ring portions of neighboring molecules are involved in the self-association process. Thermal denaturation studies demonstrate that both BePI and BgPI preferentially bind and stabilize triple-helical relative to double-helical DNA, the latter ligand doing so to a greater extent than the former. Binding to either double-helical or triple-helical polydeoxynucleotides quenches the fluorescence of both ligands, with the greatest degree of quenching accompanying binding to triplex relative to duplex DNA. In addition, binding to either duplex or triplex DNA quenches the fluorescences of BgPI to a substantially greater extent than that of BePI. Viscosity studies are consistent with the conclusion that both ligands bind DNA by intercalation.