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Techniques in Molecular Biology pp 274–287Cite as

DNA Footprinting and Related Techniques for Analysing Protein-DNA Interactions

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Abstract

DNA binding proteins have attracted the attention of molecular biologists during the past few years, after it became clear that, both in prokaryotes and in eukaryotes, control of gene expression is often mediated by the interaction of regulatory proteins with defined DNA sequences.1,2 A comparison of the DNA binding sites of several prokaryotic regulatory proteins reveals a helix-turn-helix motif that exhibits a high degree of conservation in the primary structure and is supposed to interact with the B-form of the DNA double helix.1 The DNA sequences that are recognised by these regulatory proteins also show a striking similarity, independently of whether they mediate positive or negative modulation of transcription — in other words, activation or repression of genes.3 In addition, these DNA sequences exhibit limited inverted symmetry, reflecting the dimeric nature of the regulatory proteins.4 From these and similar data the idea of a ‘recognition code’ or a ‘regulatory code’ is arising, which implies the existence of a set of limited rules governing the interaction of the amino acid side-chains in regulatory proteins with the edges of the base pairs in the DNA double helix.1,5

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Further Reading

  • Berg, O.G., Winter, R.B. and Hippel, P.H. von (1981) Diffusion-driven Mechanism of Protein Translocation on Nucleic Acids. 1. Models and Theory, Biochemistry, 20, 6929–6948

    Article  Google Scholar 

  • Bourgeois, S. (1971) Techniques to Assay Repressors, in Methods in Enzymology, 21, pp. 491–500 (Academic Press, London)

    Google Scholar 

  • Dickerson, R.E. and Drew, H.R. (1981) Structure of a B-DNA Codecamer. II. Influence of Base Sequence and Helix Structure, J. Mol. Biol., 149, 761–786

    Article  Google Scholar 

  • Hippel, P.H. von and McGhee, J.D. (1972) DNA-Protein Interactions, Ann. Rev. Biochem., 41, 231–263

    Article  Google Scholar 

  • Jovin, T.M. (1976) Recognition Mechanisms of DNA Specific Enzymes, Ann. Rev. Biochem., 45, 889–920

    Article  Google Scholar 

  • Ohlendorf, D.H., Anderson, W.F., Fisher, R.G., Takeda, Y. and Matthews, B.W. (1982). The Molecular Basis of DNA-Protein Recognition Inferred from the Structure of cro Repressor, Nature, Lond., 298, 718–723

    Article  Google Scholar 

  • O’Neill, M.C. (1976) Similarities in the Helical Sequences of the Repressor-binding Sites in the lac and Lambda Operators, Nature, Lond., 260, 550–554

    Article  Google Scholar 

  • Rein, R., Kieber-Emmons, T., Haydock, K., Garduno-Juarez, R. and Shibata, M. (1983) Molecular Modelling of Protein-Nucleic Acid Interactions, J. Biomol. Str. Dynam., 1, 1051–1079

    Google Scholar 

  • Sadler, F.R., Waterman, M.S. and Smith, T.F. (1983) Regulatory Pattern Identification in Nucleic Acid Sequences, Nucleic Acids Res., 11, 2221–2231

    Article  Google Scholar 

  • Seeman, N.C., Rosenberg, J.M. and Rich, A. (1976) Sequence-specific Recognition of Double Helical Nucleic Acids by Proteins, Proc. Natl. Acad. Sci. USA, 73, 804–808

    Article  Google Scholar 

  • Steitz, T.A., Ohlendorf, D.H., McKay, D.B., Anderson, W.F. and Matthews, B.W. (1982) Proc. Natl. Acad. Sci. USA, 79, 3097–3100

    Article  Google Scholar 

References

  1. Pabo, C.O. and Sauer, R.T. (1984) Protein-DNA Recognition, Ann. Rev. Biochem., 53, 293–321

    Article  Google Scholar 

  2. Dynan, W.S. and Tjian, R. (1985) Control of Eukaryotic mRNA Synthesis by Sequence-specific DNA-binding Proteins, Nature, Lond., 316, 774–778

    Article  Google Scholar 

  3. Gicquel-Sanzey, B. and Cossart, P. (1982) Homologies Between Different Procaryotic DNA-binding Regulatory Proteins and Between Their Sites of Action, EMBO J., 1, 591–595

    Google Scholar 

  4. Takeda, Y., Ohlendorf, D.H., Anderson, W.F. and Matthews, B.W. (1983) DNA Binding Proteins, Science, 221, 1020–1026

    Article  Google Scholar 

  5. Beato, M. (1985) Modulation of Gene Expression Through DNA-binding Proteins: Is There a Regulatory Code?, in Neth, Gallo, Greaves, and Janka, (eds), Modern Trends in Human Leukemia, VI, pp. 217–223 (Springer-Verlag, Berlin)

    Google Scholar 

  6. Galas, D.J. and Schmitz, A. (1978) DNase Footprinting: A Simple Method for the Detection of Protein-DNA Binding Specificity, Nucleic Acids Res., 5, 3157–3170

    Article  Google Scholar 

  7. Ogata, R.T. and Gilbert, W. (1978) An Amino-terminal Fragment of the lac Repressor Binds Specifically to the lac operator, Proc. Natl. Acad. Sci. USA, 75, 5851–5854

    Article  Google Scholar 

  8. Siebenlist, U., Simpson, R.B. and Gilbert, W. (1980) E. Coli RNA Polymerase Interacts Homologously with Two Different Promoters, Cell, 20, 269–281

    Article  Google Scholar 

  9. Church, G.M. and Gilbert, W. (1984) Genomic Sequencing, Proc. Natl. Acad. Sci. USA, 81, 1991–1995

    Article  Google Scholar 

  10. Jackson, P.D. and Felsenfeld, G. (1985) A Method for Mapping Intranuclear Protein-DNA Interactions and its Application to a Nuclease Hypersensitive Site, Proc. Natl. Acad. Sci. USA, 82, 2296–2230

    Article  Google Scholar 

  11. Riggs, A.D., Suzuki, H. and Bourgeois, S. (1970) lac Repressor-Operator Interactions, J. Mol. Biol. 48, 67–83

    Article  Google Scholar 

  12. Geisse, S., Scheidereit, C., Westphal, H.M., Hynes, N.E., Groner, B. and Beato, M. (1982) Glucocorticoid Receptors Recognize DNA Sequences in and Around Murine Mammary Tumour Virus DNA, EMBO J., 1, 1613–1619

    Google Scholar 

  13. Fried, M. and Crothers, D.M. (1981) Equilibria and Kinetics of lac Repressor-Operator Interactions by Polyacrylamide Gel Electrophoresis, Nucleic Acids Res., 9, 6505–6525

    Article  Google Scholar 

  14. Garner, M.M. and Revzin, A. (1981) A Gel Electrophoretic Method for Quantifying the Binding of Proteins to Specific DNA Regions. Application to Components of the E. coli Lactose Operon Regulatory System, Nucleic Acids Res., 9, 3047–3060

    Article  Google Scholar 

  15. Strauss, F. and Varshavsky, A. (1984) A Protein Binds to a Satellite DNA Repeat at Three Specific Sites That Would be Brought into Mutual Proximity by DNA Folding in the Nucleosome, Cell, 37, 889–901

    Article  Google Scholar 

  16. Topol, J., Ruden, D.M. and Parker, CS. (1985) Sequences Required for in vitro Transcriptional Activation of a Drosophila hsp 70 gene, Cell, 42, 527–537

    Article  Google Scholar 

  17. Bowen, B., Steinberg, J., Laemmli, U.K. and Weintraub, H. (1980) The Detection of DNA-binding Proteins by Protein Blotting, Nucleic Acids Res., 8, 1–20

    Article  Google Scholar 

  18. White, B.A., Preston, G.M., Lufkin, T.C. and Bancroft, C. (1985) Detection of Two Chromatin Proteins Which Bind Specifically to the 5′-flanking Region of the Rat Prolactin Gene, Mol. Cell. Biol., 5, 2967–2974

    Google Scholar 

  19. Scheidereit, C., Geisse, S., Westphal, H.M. and Beato, M. (1983) The Glucocorticoid Receptor Binds to Defined Nucleotide Sequences Near the Promoter of Mouse Mammary Tumour Virus, Nature, Lond., 304, 749–752

    Article  Google Scholar 

  20. Levens, D. and Howley, P.M. (1985) Novel Method for Identifying Sequence-specific DNA-binding Proteins, Mol. Cell Biol., 5, 2307–2315

    Google Scholar 

  21. Shalloway, D., Kleinberger, T. and Livingston, D.M. (1980) Mapping of SV40 DNA Replication Origin Region Binding Sites for the SV40 T-antigen by Protection Against Exonuclease III Digestion, Cell, 20, 411–422

    Article  Google Scholar 

  22. Wu, C. (1984) Two Protein-binding Sites in Chromatin Implicated in the Activation of Heat-shock Genes, Nature, Lond., 309, 229–234

    Article  Google Scholar 

  23. Wu, C. (1985) An Exonuclease Protection Assay Reveals Heat-shock Element and TATA Box DNA-binding Proteins in Crude Nuclear Extracts, Nature, Lond., 317, 84–87

    Article  Google Scholar 

  24. Wu, C. (1980) The 5′ Ends of Drosophila Heat-shock Genes in Chromatin are hypersensitive to DNasel, Nature, Lond., 286, 854–861

    Article  Google Scholar 

  25. Nedospasov, S.A. and Georgiev, G.P. (1980) Non-random Cleavage of SV40 DNA in the Compact Minichromosome and Free in Solution by Micrococcal Nuclease, Biochim. Biophys. Res. Comm., 92, 532–539

    Article  Google Scholar 

  26. Gralla, J.D. (1985) Rapid Footprinting on Supercoiled DNA, Proc. Natl. Acad. Sci. USA, 82, 3078–3081

    Article  Google Scholar 

  27. Cartwright, I.L., Hertzberg, R.P., Dervan, P.B. and Elgin, S.C.R. (1983) Cleavage of Chromatin with Methidiumpropyl-EDTA-iron(II), Proc. Natl. Acad. Sci. USA, 80, 3213–3217

    Article  Google Scholar 

  28. Maxam, A. and Gilbert, W. (1980) Sequencing End-labelled DNA, in Methods in Enzymology, 65, pp. 499–560 (Academic Press, London)

    Google Scholar 

  29. Ahe, D. von der, Renoir, J-M., Buchou, T., Baulieu, E-E. and Beato, M. (1986) Receptors for Glucocorticosteroid and Progesterone Recognize Distinct Features of a DNA Regulatory Element, Proc. Natl Acad. Sci. USA, 83, 2817–2821

    Article  Google Scholar 

  30. Scheidereit, C. and Beato, M. (1984) Contacts between Receptor and DNA Double Helix Within a Glucocorticoid Regulatory Element of Mouse Mammary Tumor Virus, Proc. Natl Acad. Sci. USA, 81, 3029–3034

    Article  Google Scholar 

  31. Herr, W. (1985), Diethyl Pyrocarbonate: A Chemical Probe for Secondary Structure in Negatively Supercoiled DNA, Proc. Natl. Acad. Sci. USA, 82, 8009–13

    Article  Google Scholar 

  32. Wharton, R.P. and Ptashne, M. (1985), Changing the Binding Specificity of a Repressor by Redesigning an o-helix. Nature, Lond., 316, 601–605

    Article  Google Scholar 

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Authors
  1. Miguel Beato
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Editors and Affiliations

  1. Division of Biological and Environmental Sciences, The Hatfield Polytechnic, PO Box 109, College Lane, Hatfield, Hertfordshire, AL10 9AB, England

    John M. Walker (Principal Lecturer in Biochemistry) (Principal Lecturer in Biochemistry)

  2. Department of Infectious Diseases, Section of Bacteriology, University of Utrecht, PO Box 80.171, 3508 TD, Utrecht, The Netherlands

    Wim Gaastra (Associate Professor of Microbiology) (Associate Professor of Microbiology)

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© 1987 John M. Walker and Wim Gaastra

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Beato, M. (1987). DNA Footprinting and Related Techniques for Analysing Protein-DNA Interactions. In: Walker, J.M., Gaastra, W. (eds) Techniques in Molecular Biology. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-9799-5_15

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  • DOI: https://doi.org/10.1007/978-1-4615-9799-5_15

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-7099-3673-2

  • Online ISBN: 978-1-4615-9799-5

  • eBook Packages: Springer Book Archive

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