Mechanism of intercalation: Ion effects on the equilibrium and kinetic constants for the interaction of propidium and ethidium with DNA

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Abstract
The effects of sodium ion concentration on the binding isotherms and association and dissociation reaction rates for the interaction of the closely related intercalating dication, propidium, and the monocation, ethidium, with DNA have been determined by spectrophotometric binding and stopped‐flow kinetics methods. The binding of propidium to DNA is best described by a neighbor‐exclusion binding isotherm (two base pairs per binding site) with negative ligand cooperatively on binding. The cooperativity parameter is fairly independent of salt concentration, while the log of the observed equilibrium binding constant varies with −log [Na+], with a slope of two for the propidium–DNA interaction. These effects of the sodium ion on the equilibrium binding of propidium with DNA are similar to those previously described for the dication, quinacrine [Wilson, W.D. & Lopp, I.G. (1979) Biopolymers, 18, 3025–3041]. Ethidium behaves, as a function of salt, as a monocation binding to DNA with neighbor exclusion and without ligand cooperativity. Equations are derived for two limiting kinetics models for intercalation involving binding of the intercalator to a preequilibrium, open state of DNA (model I) or binding form a preequilibrium externally associated state of the intercalator with DNA (model II). Model II gives the best fit to all of the kinetic results if it is assumed that the initial external interaction of the intercalator with DNA is similar to the exchange of free and condensed simple counterions. Intercalation then occurs from this state following an opening transition of the base pairs of the double helix. This model predicts a larger effect of salt concentration on the association than on the dissociation reaction, and that is what is experimentally observed. The intercalation conformational change makes a significant contribution to the ionic effects for both the equilibrium binding and the kinetic constants. The dissociation results and the association reaction results under pseudo‐first‐order conditions could be fit with single exponential curves under the conditions of our experiments.

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