The Gel Shift Assay for the Analysis of DNA-Protein Interactions

The gel shift assay is one of the most powerful methods for the analysis of DNA-protein interactions (1 ,2 ). The assay itself is simple. DNA and protein are mixed together, the solution subjected to electrophoresis through polyaerylamide, and the gel is then analyzed for DNA, usually by autoradiography of radiolabeled DNA (3 ,4 ). Binding of the protein to the DNA can result in a complex that has a different electrophoretic mobility from the free DNA. In general, the mobility of the complex is retarded relative to the unbound DNA and thus the assay is often called gel retardation. However, with circular DNA substrates (typically, minicircles of 200–400 bp), the DNA-protein complex can migrate faster than the free DNA (5 ,6 ). The separation of the complex from the free DNA, and therefore the detection of the complex, is dependent on a variety of factors. These must be determined experimentally for each system. However, the ease with which the assay can be performed means that the optimal conditions can be discovered quickly. Factors that influence the electrophoretic mobility of DNA-protein complexes include the molecular weight of the protein and the DNA (7 ,8 ), the ionic strength and the pH of the electrophoresis buffer (9 ), the concentration of the gel matrix, and the temperature. Particularly useful accounts of how modifications to the assay can affect the mobility of DNA-protein complexes have been published (2 ,10 ).