Influence of different counterions on the fluorescent probe-DNA complex

Studies carried out on both linear and covalently closed DNA have clearly revealed at least two different types of probe-DNA complexes depending on the different experimental procedure adopted, and two main types of binding of the probe have been clearly established and referred to as intercalative and external binding. In order to investigate the influences of the different counterions on the stability of the probe-DNA complex, a set of static fluorimetric measurements were performed in a wide range of concentrations (1 mM to 2 M) of different alkaline-earth chlorides. At low salt concentrations (in the range of millimolar values) no detectable fluorescence intensity changes were evidenced by the use of alkaline salts, but a marked decrease was detected by using alkaline-earth salts. The present work investigates moreover the role played by the different salt, in first place Calcium salts, on the stability of ethidium-DNA complex, by the use of the static fluorimetric titration procedure which is able to discriminate between the two strong and weak binding sites on DNA. Our experimental results have been interpreted in terms of a peculiar Calcium-DNA interaction, involving not only the electrostatic charges of phosphate moiety but also the aromatic rings of the bases, i.e., the intercalation sites on double helix DNA.