Volume and hydration changes of DNA–ligand interactions Original Research Article

We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA)•poly(dT), poly[d(A–T)]•poly[d(A–T)], and poly[d(G–C)]•poly[d(G–C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A–T)]•poly[d(A–T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute–solute H-bonds, and III. disruption of “structural” hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA–ligand interactions.