Summary
Various methodologies have been developed for the detection of DNA-binding activities and the identification of the “footprints” of a protein on DNA. The most widely used footprinting techniques employ reagents such as deoxyribonuclease I (DNase I) and dimethyl sulfate (DMS) for protection analysis in solution. Nevertheless, these techniques have several disadvantages, and although these may be bypassed by coupling the footprinting reaction with an electrophoretic mobility-shift assay (EMSA), the size and the sequence specificity of DNase I and DMS as well as the problem of protein exchange during the footprinting reaction pose significant limitations. These limitations can be circumvented by combining the advantages of EMSA, with the subsequent exposure of the resolved DNA–protein complex(es) to the chemical nuclease 1,10-phenanthroline–copper ion (OP–Cu) while they are still embedded in the polyacrylamide matrix (in-gel assay).
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References
Sigman, D. S., Kuwabara, M. D., Chen, C. H., and Bruice, T. W. (1991). Nuclease activity of 1,10- phenanthroline–copper in study of protein–DNA interactions. Methods Enzymol. 208, 414–433.
Papavassiliou, A. G. (1995). Chemical nucleases as probes for studying DNA–protein interactions. Biochem. J. 305, 345–357.
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Acknowledgments
This work has profited greatly from discussions of the author with the students and teachers participating in the 1991–1996 EMBO Courses on “DNA–Protein Interactions”.
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Papavassiliou, A.G. (2009). Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_13
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