application of ultrasonic velocity techniques for the direct measurements of the hydration changes that results from the interaction of ligands to DNA

Buckin V. A., De Maeyer L., Funck Th., Kudrjashov E., Braginskaya F., Kankia B. I. and Marky L.A.

J. Biol. Struct. And Dyn., 10, pp. 21 (1993)

The ultrasonic velocity of a solution is a sensitive probe for the solute hydration binding of ligands to DNA molecules is normally accompanied by an interaction between the hydration shells of the DNA and the ligand. These hydration changes can be detected directly by following the change in the ultrasonic velocity. Recent improvements in this technique make it possible to carry out titrations using solutions containing less than 1 mg/mL of DNA with ligands directly in an ultrasonic resonator cell having a volume of less than 1 mL. These titrations allow one to assess the overall stoichiometry of the DNA-ligand complexes, as well as the binding affinities and the related hydrational structural characteristics of the complexes. We have studied the interaction of Mg2+ netropsin (a minor groove ligand) ethidium and daunmycin (intercalators) to DNA duplexes of known sequence. Titration of oligonucleotides (Cs+ salts) with Mg2+ results in a decrease of the ultrasonic velocity implying overall dehydration of the ionic atmosphere of DNA on substituting Mg2+ for Cs+. The magnitude of the dehydration depends on the DNA sequence. For larger ligands, the dehydration event depends primarily on the binding mode. In addition, the formation of secondary complexes can be detected.

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