Increased accessibility of bases In DNA upon binding of acrtdlne orange

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Abstract
Acridine orange (A0) forms 1:1 complexes with dsDNA which are Insoluble 1n aqueous media, exhibit red luminescence, have minimal green luminescence and resemble complexes of A0 with ss nucleic acids. During formation and/or dissociation of these complexes, accessibility of DNA bases to two conformational probes, formaldehyde and diethyl pyrocarbonate 1s increased, suggesting that the base pairing is destroyed and DNA at least partially denatured. Adriamydn and ElUptidne, but not Ethidium Bromide exert similar destabilizing effects. The results confirm our earlier predictions based on thermodynamic calculations that the double helix undergoes destabilization upon binding an intercalator characterized by high ccoperativity 1n Interaction with ss nucleic adds. Thus, the highly cooperative ligand binding to ss sections during the “breathing” of the polyner may progressively destabilize the adjacent ds structure.