Introduction

The interaction of proteins with nucleic acids (DNA, RNA) is central to the control of many cellular processes including DNA replication, recombination and repair, transcription, and viral assembly. One important technique for studying gene regulation and determining protein–nucleic acid interactions is the electrophoretic mobility shift assay (EMSA). An advantage of studying protein–nucleic acid interactions by an electrophoretic assay is the ability to resolve complexes of different stoichiometry or conformation. Another major advantage is that the source of the nucleic acids and proteins may be a crude nuclear or whole cell extract, in vitro transcription product or a purified preparation. EMSA can be used qualitatively to identify sequence-specific, DNA or RNA-binding proteins (such as transcription factors) in crude lysates and, in conjunction with mutagenesis, to identify the important binding sequences within the upstream regulatory region of a given gene. EMSA can also be utilized quantitatively to measure thermodynamic and kinetic parameters such as dissociation constant