Analytical Approaches for Monitoring DNA–Protein Interactions

DNA–protein interactions play a critical role in cellular regulation. We herein review existing analytical methods for investigating these interactions, highlighting methods such as chromatin immunoprecipitation and yeast-one-hybrid that are used to identify undiscovered DNA–protein interactions. We summarize the most common approaches for characterizing known interactions based on DNA–protein structure, thermodynamic and kinetic measurements, and dynamic binding assays. We discuss techniques in optical imaging as well as representative methods, such as eletrophoretic mobility shift assay and surface plasmon resonance. The advantages and disadvantages of these techniques are used to assess a proposed optical platform based on single-walled carbon nanotube (SWCNT) fluorescence.