Pentalysine-Deoxyribonucleic Acid Interactions: A Model for the General Effects of Ion Concentrations on the Interactions of Proteins with Nucleic Acids

The interaction of the oligopeptide pentalysine [(Lys)⁵] with T7 DNA has been investigated by difference boundary sedimentation velocity. The system is of interest as a model for the electrostatic component of the interactions of proteins with nucleic acids. Binding constants for (Lys)₅-T7 DNA (K_obsd^LD) have been determined as a function of [NaCL], [MgCL2], pH, and temperature, under solution conditions such that K_obsd^LD is in the range 10²-10⁵ M⁻¹. We Find that K_obsd^LD is a sensitive function of the ionic environment but is virtually independent of temperature. in particular, K_obsd^LD decreases dramatically with increasing [NaCL], Plots of log K_obsd^LD vs. log [NaCL] are linear, with slopes that decrease with increasing pH. At constant [NaCL], K_obsd^LD decreases with an increase in pH or in [MgCL2]. The data, analyzed by binding theory [Record, M. T., Jr., Lohman, T. M., & deHaseth, P. L. (1976) J. Mol. Biol. 107, 145-158; Record, M. T., Jr., Anderson, C. F., & Lohman, T. M. (1978) Q. Rev. Biophys. 11, 103-178] are consistent with an electrostatic interaction between (Lys)5 and T7 DNA, driven by the entropic contribution of counterion release to the free energy of binding. The effects of pH are explained quantitatively by using a simple titration model; as the pH is increased, the net positive charge on the (Lys)₅ is reduced, and consequently both K_obsd^LD and |(∂ log K_obsd/∂ log [NaCL])_{pH T}| are reduced. The effects of MgCL2 are explained quantitatively as a competition between Mg²⁺ and (Lys)₅ for DNA sites. The lack of a temperature dependence of K_obsd^LD is consistent with the proposed entropic origin of the binding free energy. The effects of small ions on the (Lys)₅-T7 DNA binding equilibrium are similar to those observed in various specific and nonspecific protein-DNA interactions and thereby support the electrostatic interpretation of those binding data given previously. Using the (Lys)₅ and other oligopeptide binding data as points of reference, one can decompose observed binding free energies for protein-DNA interactions into electrostatic and nonelectrostatic contributions, distinguish between specific and nonspecific effects of ions on complex formation, and estimate the number of positive charges and the number and nature of titratable groups on the DNA binding site of the protein.