The electrophoretic mobility shift assay (EMSA), one of the most sensitive methods for studying the DNA-binding properties of a protein, can be used to deduce the binding parameters and relative affinities of a protein for one or more DNA sites or for comparing the affinities of different proteins for the same sites1. It is also useful for studying higher-order complexes containing several proteins, observed as a 'supershift assay'. EMSA also can be used to study protein- or sequence-dependent DNA bending2. In an EMSA, or simple 'gel shift', a 32P-labeled DNA fragment containing a specific DNA site is incubated with a candidate DNA-binding protein. The protein-DNA complexes are separated from free (unbound) DNA by electrophoresis through a nondenaturing polyacrylamide gel. The protein retards the mobility of the DNA fragments to which it binds; thus, the free DNA migrates faster through the gel than does the DNA-protein complex. An image of the gel reveals the positions of the free and bound 32P-labeled DNA.
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References
Fried, M.G. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10, 366–376 (1989).
Crothers, D.M., Gartenberg, M.R. & Schrader, T.E. DNA bending in protein-DNA complexes. Methods Enzymol. 208, 118–146 (1991).
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Electrophoretic mobility shift assays. Nat Methods 2, 557–558 (2005). https://doi.org/10.1038/nmeth0705-557
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DOI: https://doi.org/10.1038/nmeth0705-557