Abstract
Within the last few years footprinting techniques have become increasingly important in the study of protein-nucleic acid interactions. This is partly the result of a fast-growing number of known nucleic acid binding proteins but also because of an increase in the available probes that can be chosen in order to tackle a specific problem. There are two major groups of probes-the chemical probes and the enzymatic probes. These enzymatic probes, such as DNase I or exonuclease III, have the advantage of acting specifically at the DNA. Chemical probes are often less specific and react also with the protein. This can disturb the correct interaction of protein and DNA. For the study of very fragile protein-DNA complexes, therefore, enzymatic probes are often preferable.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Further Reading
Kow, Y. W. (1989) Mechanism of action of Escherichia co11 Exonuclease III. Biochemistry 28,3280–3287.
References
Rogers, S. G. and Weiss, B. (1980) Exonuclease III of Escherichia coli K-12, an AP endonuclease. Meth. Enzymol. 65,201–211.
Shalloway, D., Kleinberger, T., and Livingston, D. M. (1980) Mapping of SV 40 DNA replication origin region binding sites for the SV 40 DNA replication antigen by protection against Exonuclease III digestion, Cell 20,411–422.
Metzger, W., Schickor, P, and Heumann, H (1989) A cinematographic view of Eschenchia coli RNA polymerase translocation. EMBO J. 8,2745–2754
Pavco, P. A and Steege, D. A. (1990) Elongatton by Escherichia coli RNA polymerase is blocked in vitro by a site specific DNA binding protein. J. Biol. Chem. 265,9960–9969.
Wu, C (1985) An exonuclease protection assay reveals heat-shock element and TATA box binding proteins in crude nuclear extracts. Nature, 317,84–87.
Loh, T. P., Sievert, L. L., and Scott, R. W. (1990) Evidence for a stem cellspecific repressor of Moloney murine leukemia virus expression in embryonic carcinoma cells. Mol. Cell. Biol. 10,4045–4057
Carnevali, F., La Porta, C., Ilardi, V., and Beccari, E. (1989) Nuclear factors specifically bind to upstream sequences of a Xenopus laevis ribosomal protein gene promoter. Nucleic Acids Res. 17,8171–8184.
Fried, M. and Crothers, D M. (1981) Equilibria and kinetics of lac repressoroperator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9,6505–6525.
Heumann, H., Metzger, W., and Niehorster, M. (1986) Visualization of mtermediary transcription states in the complex between Escherichia coli DNA dependent RNA polymerases and a promoter-carrying DNA fragment using the gel retardation method. Eur. J. Biochem. 158, 575–579.
Straney, D. C. and Crothers, D. M. (1987) A stressed intermediate in the formation of stably initiated RNA chains at the Escherichiu coli lac UV 5 promoter. J. Mol. Biol. 193,267–278.
Straney, D. C. and Crothers, D M (1987) Comparison of the open complexes formed by RNA polymerase at the Escherichia coli lac UV 5 promoter. J. Mol. Biol. 193,279–292.
Gaur, N. K., Oppenheim, J., and Smith, I. (1991) The Bacillus subtilis sin gene, a regulator of alternate developmental processes, codes for a DNA-binding protein, J. Bact. 173,678–686.
Owen, R. D., Bortner, D. M., and Ostrowski, M. C. (1990) rus oncogene activatton of a VL30 transcriptional element is linked to transformation. Mol. Cell. Biol. 10, 1–9.
Wilkison, W. O., Min, H. Y, Claffey, K. P., Satterberg, B. L., and Spiegelman, B. M. (1990) Control of the adipisin gene in adipocyte differentiatton. J. Biol. Chem. 265,477–482.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Humana Press Inc.
About this protocol
Cite this protocol
Metzger, W., Heumann, H. (1994). Footprinting with Exonuclease III. In: Geoff Kneale, G. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 30. Humana Press. https://doi.org/10.1385/0-89603-256-6:11
Download citation
DOI: https://doi.org/10.1385/0-89603-256-6:11
Publisher Name: Humana Press
Print ISBN: 978-0-89603-256-9
Online ISBN: 978-1-59259-517-4
eBook Packages: Springer Protocols