Complex formation of acridine orange with single-stranded polyriboadenylic acid and 5?-AMP: Cooperative binding and intercalation between bases

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Abstract
The binding of acridine orange to single-stranded polyribonucleic acid at low polymer to dye ratios exhibits cooperative behavior of the kind observed with other simple polyanions. It is thus attributed to electrostatic interaction between polymer and stacked dye molecules. At higher polymer to dye ratios, however, distinct deviations from the predictions of the basic theory occur. These are interpreted by additional non-cooperative binding of acridine orange to the bases of the polymer subunits owing to dye-base stacking. This effect is studied also with 5′-AMP monomers where it likewise leads to complex formation. Both systems are investigated experimentally by means of the changes produced in the dye spectrum. Based on quantitative analyses the equilibrium constants of both systems are evaluated and discussed. They indicate a sandwich-type of intercalation of dye between two bases of the single-stranded polymer.