Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift

The gel mobility shift assay is routinely used to visualize protein—RNA interactions. Its power resides in the ability to resolve free from bound RNA with high resolution in a gel matrix. We review the quantitative application of this approach to elucidate thermodynamic properties of protein—RNA complexes. Assay designs for titration, competition, and stoichiometry experiments are presented for two unrelated model complexes.