Abstract
Membrane filtration has a long history in the analysis of protein-nucleic acid complex formation, having first been used to examine RNA-protein interactions (1), before being introduced to DNA-protein interaction studies by Jones and Berg in 1966 (2). The principle of the technique is straightforward. Under a wide range of buffer conditions, nucleic acids pass freely through membrane filters, whereas proteins and their bound ligands are retained. Thus, if a particular protein binds to a specific DNA sequence, passage through the filter will result in retention of a fraction of the protein-DNA complex by virtue of the protein component of the complex. The amount of DNA retained can be determined by using radioactively labeled DNA to form the complex and then determining the amount of radioactivity retained on the filter by scintillation counting. The technique can be used to analyze both binding equilibria and kinetic behavior, and if the DNA samples retained on the filter and in the filtrate are recovered for further processing, the details of the specific binding site can be probed by interference techniques.
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References
Nirenberg, M. and Leder, P. (1964) RNA codewords and protein synthesis. The effect of trinucleotides upon the binding of sRNA to ribosomes. Science 145, 1399–1407.
Jones, O. W. and Berg, P. (1966) Studies on the binding of RNA polymerase to polynucleotides. J. Mol. Biol. 22, 199–209.
Riggs, A. D., Bourgeois, S., Newby, R. F., and Cohn, M. (1968) DNA binding of the lac repressor. J. Mol. Biol. 34, 365–368.
Riggs, A. D., Suzuki, H., and Bourgeois, S. (1970) lac repressor-operator interac-tion. I. Equilibrium studies. J. Mol. Biol. 48, 67–83.
Riggs, A. D., Bourgeois, S., and Cohn, M. (1970) The lac repressor-operator interaction. III. Kinetic studies. J. Mol. Biol. 53, 401–417.
Phillips, S. E. V., Manfield, I., Parsons, I., Davidson, B. E., Rafferty, J. B., Somers, W. S., et al. (1989) Cooperative tandem binding of Met repressor from Escherichia coli. Nature 341, 711–715.
Old, I. G., Phillips, S. E. V., Stockley, P. G., and Saint-Girons, I. (1991) Regulation of methionine biosynthesis in the enterobacteriaceae. Prog. Biophys. Mol. Biol. 56, 145–185.
Ryan, P. C., Lu, M., and Draper, D. E. (1991) Recognition of the highly conserved GTPase center of 23S ribosomal RNA by ribosomal protein L1 1 and the antibiotic thiostrepton. J. Mol. Biol. 221, 1257–1268.
Wyman, J. and Gill, S. J. (1990) In Binding and Linkage: Functional Chemistry of Biological Macromolecules, chap. 2, University Science Books, Mill Valley, CA.
Siebenlist, U. and Gilbert, W. (1980) Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc. Natl. Acad. Sci. USA 77, 122–126.
Hayes, J. J. and Tullius, T. D. (1989) The missing nucleoside experiment: a new technique to study recognition of DNA by protein. Biochemistry 28, 9521–9527.
Maxam, A. M. and Gilbert, W. K. (1980) Sequencing end-labelled DNA with base-specific chemical cleavages. Methods Enzymol. 65, 499–560.
Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacterophage T4 DNA polymerase. Science 249, 505–510.
Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822.
Conrad, R. C., Giver, L., Tian, Y. and Ellington, A. D. (1996) In vitro selection of nucleic acid aptamers that bind proteins. Methods Enzymol. 267, 336–367.
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© 2001 Humana Press Inc., Totowa, NJ
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Stockley, P.G. (2001). Filter-Binding Assays. In: Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology, vol 148. Humana Press. https://doi.org/10.1385/1-59259-208-2:001
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DOI: https://doi.org/10.1385/1-59259-208-2:001
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