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Combining Gel Retardation and Footprinting to Determine Protein-DNA Interactions of Specific and/or Less Stable Complexes

Abstract : DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate, or if several different protein-DNA complexes are formed. Our protocol differs from traditional footprinting protocols, because it provides a method to isolate the protein-DNA complex from a native gel after treatment with the footprinting agent, thus removing the bound DNA from the free DNA or other protein-DNA complexes. The DNA is then extracted from the isolated complex before electrophoresis on a sequencing gel to determine the footprinting pattern. This analysis provides a possible solution for those who have been unable to use traditional footprinting methods to determine protein-DNA contacts.
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https://hal.inrae.fr/hal-03128795
Contributor : Nathalie Seguin <>
Submitted on : Tuesday, February 2, 2021 - 2:33:41 PM
Last modification on : Wednesday, May 12, 2021 - 8:17:00 AM

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Meng-Lun Hsieh, Alice Boulanger, Leslie Knipling, Deborah Hinton. Combining Gel Retardation and Footprinting to Determine Protein-DNA Interactions of Specific and/or Less Stable Complexes. Bio-protocol , Bio-protocol LCC, 2020, 10 (23), ⟨10.21769/BioProtoc.3843⟩. ⟨hal-03128795⟩

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