We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, Delta V and adiabatic compressibility, Delta K-S, that accompany the binding of netropsin to the poly(dAdT) poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) tripler. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, Delta V, and small positive changes in compressibility, Delta K-S. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, Delta V; and compressibility, Delta K-S. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) tripler causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dT) poly(dA).poly(dT) tripler. In other words, netropsin binding to the homopolymeric duplex, poly(dA) poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi K-S, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., and Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol(-1) to the entropy of binding. This value correponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the tripler than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) tripler causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex. In general, we discuss the basis for relating macroscopic and microscopic properties, particularly emphasizing how measured changes in volume and compressibility can be interpreted in terms of the hydration properties of DNA structures in their ligand-free and ligand-bound states.
