Electrophoretic analysis of multiple protein-DNA interactions
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Updated: Oct 28, 2026

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1Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA. mfried@psu.edu
Abstract:
Under favorable conditions, native gel electrophoresis allows the resolution of protein-DNA complexes that differ in stoichiometry, identities of occupied DNA sequences (configuration), and macromolecular conformation. This technique provides a unique opportunity to analyze, in thermodynamic terms, the molecular interactions that govern the equilibrium distributions of species in protein-DNA mixtures. Here we describe a general theoretical approach to the analysis of electrophoretic band intensities, and provide examples of its application to the analysis of several interacting systems.
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