Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems

This review describes the thermodynamically rigorous analyses of spectroscopic approaches to study protein-nucleic acid interactions, including multiple-ligand binding phenomena to obtain model-independent binding isotherms and the analyses of spectroscopic stopped-flow kinetic approaches used to examine mechanisms of protein-nucleic acid interactions with emphasis on the properties of the reaction intermediates. The discussion focuses on the fundamental problem of obtaining thermodynamic, spectroscopic, and kinetic parameters free of assumptions about the relationship between the observed signal and the degree of protein or nucleic acid saturation. Topics discussed include the direct versus indirect methods in studying protein-nucleic acid interactions and the thermodynamic bases of quantitative equilibrium spectroscopic titrations.