Electrophoretic mobility shift assay

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This assay permits testing of specific binding of proteins to DNA fragments. DNA that is bound to protein will migrate slower in a nondenaturing polyacrylamide gel than unbound DNA during electrophoresis.

Most protocols rely on 32P labelling of the DNA fragment. However, it is also possible to detect the DNA via nonradioactive detection methods (like fluorescence). Ethidium bromide staining is generally not sensitive enough since usually small amounts of DNA are used in this assay.

Specific Protocols

Knight:Electrophoretic mobility shift assay


Background information

  1. EMSA by Pierce
  2. Electrophoretic mobility shift assay from Wikipedia


  1. Jing D, Beechem JM, and Patton WF. . pmid:15300760. PubMed HubMed [Jing-Electrophoresis-2004]
  2. Jing D, Agnew J, Patton WF, Hendrickson J, and Beechem JM. . pmid:12872218. PubMed HubMed [Jing-Proteomics-2003]
All Medline abstracts: PubMed HubMed


  1. Mobility Shift DNA-Binding Assay Using Gel Electrophoresis from Current Protocols in Molecular Biology
  2. Gel Retardation Assays for DNA-binding Proteins from Molecular Cloning


  1. EMSA kit from Invitrogen
    • primary advantage is that this protocol doesn't require use of radioactivity or prelabelling of DNA, sensitivity is questionable however
    • Also see relevant papers [1, 2].
  2. LightShift Chemiluminescent EMSA Kit from Pierce
    • claimed to be more sensitive than radioactive and digoxigenin methods
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