Linkage between proton binding and folding in RNA: A thermodynamic framework and its experimental application for investigating pKa shifting

Perturbation of p K a values can change the favored protonation states of the nucleobases at biological pH and thereby modulate the function of RNA and DNA molecules. In an effort to understand the driving forces for p K a shifting specific to nucleic acids, we developed a thermodynamic framework that relates proton binding to the nucleobases and the helix–coil transition. Key features that emerge from the treatment are a comprehensive description of all the actions of proton binding on RNA folding: acid and alkaline denaturation of the helix and p K a shifting in the folded state. Practical experimental approaches for measuring p K a s from thermal denaturation experiments are developed. Microscopic p k a values (where k a is the acid dissociation constant) for the unfolded state were determined directly by experiments on unstructured oligonucleotides, which led to a macroscopic p K a for the ensemble of unfolded states shifted toward neutrality. The formalism was then applied to pH-dependent UV melting data for model DNA oligonucleotides. Folded-state p k a values were in good agreement with the outcome of pH titrations, and the acid and alkaline denaturation regions were well described. The formalism developed here is similar to that of Draper and coworkers for Mg 2+ binding to RNA, except that the unfolded state is described explicitly owing to the presence of specific proton-binding sites on the bases. A principal conclusion is that it should be possible to attain large p K a shifts by designing RNA molecules that fold cooperatively.