Summary
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.
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Acknowledgments
We thank Ivan Baxter for the alkaline hydrolysis protocol and Dana Abramovitz for generation of the GLD-1 expression construct. S.P.R. was supported by a Damon Runyon Cancer Research Foundation Fellowship (DRG-1723). M.I.R was supported by a Research Scholar grant from the American Cancer Society (PF-01-087-01-GMC). This research was supported by grants from the National Institutes of Health (NIH GM53320 and GM53757).
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Ryder, S.P., Recht, M.I., Williamson, J.R. (2008). Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift. In: Lin, RJ. (eds) RNA-Protein Interaction Protocols. Methods in Molecular Biology, vol 488. Humana Press. https://doi.org/10.1007/978-1-60327-475-3_7
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DOI: https://doi.org/10.1007/978-1-60327-475-3_7
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