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Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4‐p53 binding DNA as a model system
Author(s) -
Heffler Michael A.,
Walters Ryan D.,
Kugel‡ Jennifer F.
Publication year - 2012
Publication title -
biochemistry and molecular biology education
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.34
H-Index - 39
eISSN - 1539-3429
pISSN - 1470-8175
DOI - 10.1002/bmb.20649
Subject(s) - dna , electrophoretic mobility shift assay , dissociation constant , dissociation (chemistry) , electrophoresis , dna binding protein , chemistry , gel electrophoresis , biophysics , equilibrium constant , microbiology and biotechnology , biochemistry , biology , transcription factor , gene , receptor
An undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant ( K D ) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel; the DNA migrates more slowly when bound to a protein. To determine a K D the amount of unbound and protein‐bound DNA in the gel is measured as the protein concentration increases. By performing this experiment, students will be introduced to making affinity measurements and gain experience in performing quantitative EMSAs. The experiment describes measuring the K D for the interaction between the chimeric protein GAL4‐p53 and its DNA recognition site; however, the techniques are adaptable to other DNA binding proteins. In addition, the basic experiment described can be easily expanded to include additional inquiry‐driven experimentation. © 2012 by The International Union of Biochemistry and Molecular Biology