The osmotic sensitivity of netropsin analogue binding to DNA

Abstract

The binding of a netropsin analogue to random sequence DNA, monitored by CD, is seen dependent on the concentration of neutral solutes. The binding free energy decreases linearly with solute osmolal concentration and the magnitude of the effect is insensitive to the chemical identity of the solute for betaine, sorbitol, and triethylene glycol. These solutes appear to modulate binding through their effect on water activity and changes in the hydration of the drug and DNA in the complex reaction, not through a direct interaction with the reactants or the product. The dependence of binding constant on solute concentration can be interpreted as an additional binding of some 50-60 extra solute excluding water molecules by the complex. A water sensitivity of drug binding is further seen from the dependence of binding constants on the type of anion in solution. Anions in the Hofmeister series strongly affect bulk water free energies and entropies. The differences in netropsin analogue binding to DNA with Cl-, F-, and ClO4- are consistent with the effect observed with neutral solutes. The ability to measure changes in water binding associated with a specific DNA interaction is a first step toward correlating changes in hydration with the strength and specificity of binding.

The Water Effect on Allosteric Regulation of Hemoglobin Probed in Water/Glucose and Water/Glycine Solutions

“…By using two different model approaches, the Wyman linkage equation or the Gibbs Duhem equation, we found that 65-72 1 water molecules are linked to the binding of four oxygen molecules to human Hb under the experimental conditions used. Furthermore, this hydration change was found to be in agreement with the difference between the solvent-accessible surface areas of deoxy-and oxy-Hb computed from x-ray structures by Clothia et al (5,6).The experimental approach and analyses originally used by us to assess and quantify the role of water on the allosteric control of Hb have been tested in several other biochemical systems (7)(8)(9)(10)(11)(12)(13)(14). A standard linear dependence of equilibrium and kinetic free energy parameters on water activity rather than solute activity has been lately reported.…”

Probing the role of water in protein conformation and function

“…(d ) Water as a less mobile part of molecular structure In DNA-drug (Sidorova & Rau 1995) and protein-DNA interactions, the stability of the complexes are osmotically sensitive. Even the specificity of the restriction enzyme EcoR1 is dependent on its osmotic environment (Robinson & Sligar 1993;Sidorova & Rau 1996).…”

Changes in solvation during DNA binding and cleavage are critical to altered specificity of the Eco RI endonuclease

“…Application of osmotic pressure is clearly a useful and versatile technique for studying the role of water in molecular recognition and is readily applied to the study of protein-DNA interactions (22,23,29,33). Typically application of osmotic stress favors formation of the protein-DNA complex, because a sizable dehydration of both molecules accompanies binding (22,23,33).…”

“…Typically application of osmotic stress favors formation of the protein-DNA complex, because a sizable dehydration of both molecules accompanies binding (22,23,33). In the rare situations where water binding accompanies formation of the complex, osmotic stress weakens the interaction (29).…”