Detection of Protein-Nucleic Acid Interaction by Electrophoretic Mobility Shift Assay

Electrophoretic Mobility Shift Assay (EMSA) is a powerful technique for studying nucleic acid and protein interactions. This technique is based on the principle that nucleic acid-protein complex and nucleic acid migrate at different rates due to differences in size and charge. Nucleic acid and protein interactions are fundamental to various biological processes, such as gene regulation, replication, transcription, and recombination. Transcription factors and DNA interaction regulate gene expression. Homeobox (Hox) genes encode a family of transcription factors and are essential during embryonic development. Understanding the specific interactions between Hox proteins and their DNA targets is critical for elucidating the mechanisms underlying their regulatory functions.This chapter explains the principles and methodologies of EMSA in the context of Hox genes. This chapter includes detailed experimental design, including the formulation of reagents, labeling DNA probes, preparation of nuclear extracts/recombinant proteins, and binding conditions. The step-by-step protocol has been provided as an initial reference point to help a researcher conduct EMSA.