Study on the binding nature of acridine orange to DNA by means of flow dichroism.

Abstract

Abstract The binding nature of acridine orange to DNA was studied by means of equilibrium dialysis and flow dichroism with spectrophotometric analysis. The adsorption isotherm of the acridine orange-DNA system was obtained by means of equilibrium dialysis. From the experiment, the binding constant (K) and the fractional amount of the binding site to the total number of nucleotides (f) were estimated for native- and heat-denatured DNA. Under a shear gradient, the acridine orange-DNA complex showed a negative dichroism in visible region as well as in the ultraviolet region. This implies that acridine orange is oriented on DNA rather perpendicularly to its main axis, like base pairs. The magnitude of the dichroism of the complex at 500 mμ, near the visible absorption peak of acridine orange, was larger than each value of the complex and that of the DNA itself (260 mμ). The transition moment corresponding to the absorption at 500 mμ may be oriented in a more orderly manner and/or more nearly perpendicularly to the main axis of DNA than that corresponding to 260 mμ.