Salt dependence of the free energy, enthalpy, and entropy of nonsequence specific DNA binding

We used isothermal titration calorimetry to measure the effect of salt concentration on the thermodynamics for the nonsequence specific binding of the Sso7d protein to double-stranded poly(dGdC). Calorimetric isotherms for this equilibrium could be fit to a noncooperative McGhee-von Hippel model containing The enthalpy of binding (Delta N(obs)degrees), association constant (K-obs), and binding site size on DNA (n = 4.5 +/- 0.3 DNA base pairs per bound protein) as adjustable parameters. The salt dependence of the thermodynamics was determined at 25 degrees C and pH 7.6 for the addition of 20-100 mM NaCl in 10 mM sodium phosphate and 20 mM Tris-HCl buffers and for the addition of 2-10 mM MgCl2 in 20 mM Tris-HCl buffer. Salt dependences of The binding free energy (Delta G(obs)(degrees)) were quantified as the derivative SKobs = partial derivative ln(K-obs)/partial derivative ln[MX] = (1/RT) partial derivative Delta G(obs)(degrees)/partial derivative ln[MX], where [MX] is the salt concentration. SKobs values of -2.9 and -3.3 were measured for the addition of NaCl in Tris-HCl and sodium phosphate buffers, respectively, and Sk(obs) = -1.6 was measured for the addition of MgCl2 in Tris-HCl buffer. The salt dependences of Delta G(obs)degrees were in all cases accompanied by corresponding changes in the entropy component (-T Delta S(obs)degrees), whereas no systematic salt dependence was resolved for Delta H(obs)degrees, i.e., -0.5 < -(1/RT) partial derivative Delta H(obs)degrees/partial derivative ln[MX] < 0.5. These data are consistent with the inference that entropic effects dominate the salt dependence of protein-DNA association equilibria. Additional data obtained in buffers containing 80 mM KCl and potassium glutamate suggest that the enhanced binding affinity normally observed with glutamate is of enthalpic rather than entropic origin.