The nature of strong binding between acridine orange and deoxyribonucleic acid as revealed by equilibrium dialysis and thermal renaturation

Abstract

The strong binding of acridine orange with DNA was studied by means of equilibrium dialysis and thermal renaturation of the complex. Thermodynamic parameters for the strong binding with native and denatured DNA were calculated from the data of equilibrium dialysis. The association constant and the change of free energy were nearly equal for both types of DNA, but the changes of enthalpy and entropy were quite different. Binding to both types of DNA may be strong binding in nature, but the accompanying effects on the secondary structures of DNA would be different. It was found that the presence of acridine orange inhibits the completion of renaturation, presumably due to a stabilizing effect of the bound dye on the “wrong” base pairs as they are formed. The results support the notion that binding of acridine orange with the double helix is an intercalation into adjacent base pairs, while the binding with single strand is a partial intercalation into adjacent bases.