To characterize the role of water in protein-DNA interactions, we have studied the specificity of the EcoRI restriction endonuclease as a function of osmotic and hydrostatic pressure. The extent of cleavage by the enzyme at noncanonical (“star”) sites is shown to depend uniquely upon the osmotic pressure in the reaction as controlled by the addition of a wide variety of neutral solutes. Alteration of cleavage specificity (“EcoRI* activity”) is not uniformly correlated with any other colligative solvent property such as dielectric constant, viscosity, or water concentration. The application of hydrostatic pressure reverses the effects of osmotic pressure, restoring the natural selectivity of the enzyme for its canonical site GAATTC. This combination of observations provides compelling evidence that the site-specific recognition of canonical site DNA by EcoRI is mediated by discretely bound water molecules and that the release of these waters induces a fundamental change in the specificity of the interaction, leading to cleavage at alternative sites. This comprehensive analysis of solvent effects facilitates the unambiguous identification of structurally and functionally specific waters involved in macromolecular recognition events.
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