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Keywords:

  • Acridine dyes;
  • DNA;
  • Cells;
  • Ethidium dyes;
  • Pharmacology

Abstract

Ethidium and acridine dyes are classical model substances for studying the binding of small, pharmacologically active molecules to DNA. Intercalation between the DNA base pairs is nearly always proposed as the most important type of binding. According to our investigations, however, there is a second type of binding, which also occurs when the concentration of the bound molecules is low and will be referred to here as external or preintercalative binding. The experimental binding isotherms show that the binding constant for intercalation KS1 is considerably smaller than that for external binding KS2 (KS1 > KS2). This surprising result is not due to the binding enthalpy (ΔHmath image ≈ ΔHmath image) but to the binding entropy (ΔSmath image > ΔSmath image). Electrostatic interactions between the dye and the DNA represent the most important contribution to both types of binding; they are supplemented by hydrogen bonds and hydrophobic interactions. The behavior of a substance in living cells, however, cannot be reliably predicted from its in vitro binding to DNA. Very few substances are bound to the DNA of the nuclear chromatin in cell culture; for example, dyes often accumulate instead in the lysosomes. In some cases the dye binds specifically and very efficiently to the mitochondria of the living cell, especially to the mitochondrial membranes, the sites of oxidative phosphorylation.