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Methods for the analysis of DNA-protein interactions

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Abstract

The interaction of proteins with DNA is a central theme of molecular biology. In this article, we review some of the principal techniques currently used for the identification and characterization of DNA binding proteins, and for investigation of the molecular interactions that are responsible for the recognition of specific DNA sequences.

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References

  1. Garner, M. M. and Revzin, A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of theE. coli lactose operon.Nucleic Acids Res. 9, 3047–3060.

    Article  PubMed  CAS  Google Scholar 

  2. Fried, M. G. and Crothers, D. M. (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis.Nucleic Acids Res. 9, 6505–6525.

    Article  PubMed  CAS  Google Scholar 

  3. Brewer, A. C., Guille, M. J., Fear, D. J., Partington G. A., and Patient, R. K. (1995) Nuclear translocation of a maternal CCAAT factor at the start of gastrulation activatesXenopus GATA-2 transcription.EMBO J. 14 757–766.

    PubMed  CAS  Google Scholar 

  4. Bauerle, P. A. and Baltimore, D. (1988) Activation of DNA-binding activity in an apparently cytoplasmic precursor of NF-κB transcription factor.Cell 53, 211–217.

    Article  Google Scholar 

  5. Dale, T. C., Imam, A. M. A., Kerr, I. M., and Stark, G. R. (1989) Rapid activation by IFN-α of a latent DNA-binding protein present in the cytoplasm of untreated cells.Proc. Natl. Acad. Sci. USA 86, 1203–1207.

    Article  PubMed  CAS  Google Scholar 

  6. Whiteside, S. T. and Goodbourn, S. (1993) Signal transduction and nuclear targeting: regulation of transcription factor activity by subcellular localisation.J. Cell. Sci. 104, 949–955.

    PubMed  CAS  Google Scholar 

  7. Treisman, R. (1987) Identification and purification of a polypeptide that binds to the c-fos serum response element.EMBO J. 6, 2711–2717.

    PubMed  CAS  Google Scholar 

  8. Hofmann, J. F. X., Laroche, T., Brand, A. H., and Gasser, S. M. (1989) RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML.Cell 57, 725–737.

    Article  PubMed  CAS  Google Scholar 

  9. Perkins, N. D., Nicholas, R. H., Plumb M. A., and Goodwin G. H. (1989) The purification of an erythroid protein which binds to enhancer and promoter elements of haemoglobin genes.Nucleic Acids Res. 17, 1299–1314.

    Article  PubMed  CAS  Google Scholar 

  10. Welsh, J. and Cantor, C. R. (1984) Protein-DNA crosslinking.TIBS 9, 505–507.

    CAS  Google Scholar 

  11. Qureshi, S. A., Salditt-Georgieff, M., and Darnell, J. E., Jr. (1995) Tyrosine-phosphorylated Stat1 and Stat2 plus a 48 kDa protein all contact DNA in forming interferon-stimulated gene factor 3.Proc. Natl. Acad. Sci. USA 92, 3829–3833.

    Article  PubMed  CAS  Google Scholar 

  12. Singh, H., LeBowitz, J. H., Baldwin, A. S., and Sharp, P. A. (1988) Molecular cloning of an enhancer binding protein: isolation by screening an expression library with a recognition site DNA.Cell 52, 415–423.

    Article  PubMed  CAS  Google Scholar 

  13. Celenza, J. L. and Carlson, M. (1986). A yeast gene that is essential for release from glucose repression encodes a protein kinase.Science 233, 1175–1180.

    Article  PubMed  CAS  Google Scholar 

  14. Dale, T. C., Rosen, J. M., Guille, M. J., Lewin, A. R., Porter, A. G. C., Kerr, I. M., and Stark, G. R. (1989) Overlapping sites for constitutive and induced DNA-binding factors involved in interferon-stimulated transcription.EMBO J. 8, 831–839.

    PubMed  CAS  Google Scholar 

  15. Jones, K., Kadonaga, J., Rosenfeld, P., Kelly, T., and Tjian, R. (1987) A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication.Cell 48, 79–89.

    Article  PubMed  CAS  Google Scholar 

  16. Corthesy, B., Claret, F.-X., and Wahli, W. (1990) Estrogen receptor level determines sex-specific in vitro transcription from the vitellogenin promoter.Proc. Natl. Acad. Sci. USA 87, 7878–7882.

    Article  PubMed  CAS  Google Scholar 

  17. Leonard, M. W. and Patient, R. K. (1991) Primer extension analysis of mRNA isolated from transfected cell lines, inMethods in Molecular Biology, Vol. 7; Gene Transfer and Expression Protocols (Murray, E. J., ed.), Humana, Totowa, NJ, pp. 297–306.

    Chapter  Google Scholar 

  18. Sambrook, J., Fritsch, F. F., and Maniatis, T. (1989)Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

  19. Nizielski, S. E., Lechner, P. S., Croniger, C. M., Wang, N. D., Darlington, G. J., and Hanson, R. W. (1996) Animal-models for studying the genetic-basis of metabolic-regulation.J. Nutr. 126, 2697–2708.

    PubMed  CAS  Google Scholar 

  20. Rijkers, T., Peetz, A., and Rutler, U. (1994) Insertional mutagenesis in transgenic mice.Transgen. Res. 3, 203–215.

    Article  CAS  Google Scholar 

  21. Tsai, F.-Y., Keller, G., Kuo, F. C., Weiss, M., Chen, J., Rosenblatt, M., Alt, F. W., Strauss, E., and Orkin S. H. (1994) An early haematopoietic defect in mice lacking the transcription factor GATA-2.Nature 371, 221–226.

    Article  PubMed  CAS  Google Scholar 

  22. Thanos, D. and Maniatis, T. (1995) Virus induction of human IFN-β gene-expression requires the assembly of an enhanceosome.Cell 83, 1091–1100.

    Article  PubMed  CAS  Google Scholar 

  23. Schmitz, A. and Galas, D. J. (1978) DNaseI footprinting: a simple method for the detection of protein-DNA binding specificity.Nucleic Acids Res. 5, 3157–3170.

    Article  PubMed  Google Scholar 

  24. Le Blanc, C. B. and Moss, T. (1994) DNaseI footprinting, inMethods in Molecular Biology, Vol. 30; DNA-Protein Interactions. (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 1–11.

    Google Scholar 

  25. Fairall, L. M. and Rhodes, D (1992) A new approach to the analysis of DNaseI footprinting data and its application to the TFIIIA/5S DNA complex.Nucleic Acids Res. 20, 4727–4731.

    Article  PubMed  CAS  Google Scholar 

  26. Wu, C. (1985) An exonuclease protection assay reveals heat-shock element and TATA box binding proteins in crude nuclear extracts.Nature 317, 84–87.

    Article  PubMed  CAS  Google Scholar 

  27. Decker, T., Lew, D. J., Mirkovitch, J., and Darnell, J. E., Jr. (1991) Cytoplasmic activation of GAF, an IFN-γ regulated DNA-binding factor.EMBO. J. 10, 927–932.

    PubMed  CAS  Google Scholar 

  28. Loh, T. P., Sievert L. L., and Scott, R. W. (1990) Evidence for a stem cell-specific repressor of moloney leukaemia virus expression in embryonic carcinoma cells.Mol. Cell. Biol. 10, 4045–4057.

    PubMed  CAS  Google Scholar 

  29. Shafer, G. E., Price M. A., and Tullius Th. D. (1989) Use of hydroxyl radical and gel electrophoresis to study DNA structure.Electrophoresis 10, 397–404.

    Article  PubMed  CAS  Google Scholar 

  30. Shaw, P. E. and Stewart, A. F. (1994) Identification of Protein-DNA contacts with Dimethyl Sulphate, inMethods in Molecular Biology, Vol. 30; DNA-Protein Interactions (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 79–95.

    Chapter  Google Scholar 

  31. Papavasillou, A. G. (1994) 1,10 phenanthroline-copper ion nuclease footprinting of DNA-protein complexes in situ following mobility shift electrophoresis assays, inMethods in Molecular Biology, Vol. 30; DNA-Protein Interactions. (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 43–78.

    Chapter  Google Scholar 

  32. Flanagan, W. M., Papavassiliou, A. G., Rice, M., Hecht, L. B., Silverstein, S., and Wagner, E. K. (1991) Analysis of the Herpes Simplex Virus type 1 promoter controlling the expression of UL38, a true late gene involved in capsid assembly.J. Virol. 65, 769–786.

    PubMed  CAS  Google Scholar 

  33. Mernagh, D. R. and Kneale, G. G. (1996) High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.Nucleic Acids Res. 24, 4853–4858.

    Article  PubMed  CAS  Google Scholar 

  34. Cheng, X., Kumar, S., Posfai, J., Plugrath, J. W., and Richards, R. J. (1994) HhaI methyltransferase flips its target base out of the DNA helix.Cell 76, 357–369.

    Article  PubMed  Google Scholar 

  35. Lavoie, B. D., Chan, B. S., Allison, R. G., and Chaconas, G. (1991) Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the Mu type I transpososome.EMBO J. 10, 3051–3059.

    PubMed  CAS  Google Scholar 

  36. Becker, P. B., Ruppert, S., and Schutz, G. (1987) Genomic footprinting reveals cell type-specific binding of ubiquitous factors.Cell 51, 435–443.

    Article  PubMed  CAS  Google Scholar 

  37. Mueller, P. R. and Wold, B. (1989) In vivo foot-printing of muscle specific enhancer by ligation-mediated PCR.Science 246, 780–786.

    Article  PubMed  CAS  Google Scholar 

  38. Pfeifer, G. P., Steigerwald, D., Mueller, B., Wold, B., and Riggs, A. D. (1989). Genomic sequencing and methylation analysis by ligation-mediated PCR.Science 246, 810–813.

    Article  PubMed  CAS  Google Scholar 

  39. Hornstra, I. K. and Yang, T. P. (1992) Multiple in vivo footprints are specific to the active allele of the X-linked human hypoxanthine phosphoribosyltransferase gene 5′ region: implications for X chromosome inactivation.Mol. Cell. Biol. 12, 5345–5354.

    PubMed  CAS  Google Scholar 

  40. Manfield, I. and Stockley, P. G. (1994) Ethylation interference, inMethods in Molecular Biology, Vol. 30; DNA—Protein Interactions (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 125–139.

    Google Scholar 

  41. Chalepakis, G. and Beato, M. (1989) Hydroxy radical interference: a new method for the study of protein-DNA interaction.Nucleic Acids Res. 17, 1783.

    Article  PubMed  CAS  Google Scholar 

  42. Hayes, J. J. and Tullius, Th. D. (1989) The missing nucleoside experiment: a new technique to study recognition of DNA by protein.Biochemistry 28, 9521–9527.

    Article  PubMed  CAS  Google Scholar 

  43. Schickor, P., Metzger, W., Werel, W., Lederer, H., and Heumann, H. (1990) Topography of Intermediates In Transcription Initiation ofE. coli.EMBO J. 9, 2215–2220.

    PubMed  CAS  Google Scholar 

  44. Shaw, P. E., Schroter, H., and Nordheim, A. (1989) The ability of a ternary complex to form over the serum response element correlates with serum inducibility of the human c-fos promoter.Cell 56, 562–572.

    Article  Google Scholar 

  45. Phillips, S. E. V., Manfield, I., Parsons, I., Davidson, B. E., Rafferty, J. B., Somers, W. S., Margarita, D., Cohen, G. N., Saint-Gorins, I., and Stockley, P. G. (1989) Cooperative tandem binding of Met repressor fromE. coli.Nature 341, 711–715.

    Article  PubMed  CAS  Google Scholar 

  46. Bushman F. D., Anderson, J. E., Harrison, S. C. and Ptashne, M. (1985) Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator.Nature 316, 651–653.

    Article  PubMed  CAS  Google Scholar 

  47. Newman, P. C., Nwosu, V. U., Williams, D. M., Cosstick, R., Seela, F., and Connolly, B. (1990) Incorporation of a complete set of deoxyadenosine and thymidine analogues suitable for the study of protein-nucleic acid interactions into oligodeoxynucleotides. Application to theEcoRV restriction endonuclease and modification methylase.Biochemistry 29, 9891–9901.

    Article  PubMed  CAS  Google Scholar 

  48. Gogos, J. A., Tzertzinis, G., and Kafatos, F. C. (1991) Binding site selection analysis of protein-DNA interactions via solid phase sequencing of oligonucleotide mixtures.Nucleic Acids Res. 19, 1449–1453.

    Article  PubMed  CAS  Google Scholar 

  49. Gogos, J. A. and Kafatos, F. C. (1994) Determination of sequence preferences of DNA binding proteins using pooled solid-phase sequencing of low degeneracy oligonucleotide mixtures, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions. (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 295–312.

    Chapter  Google Scholar 

  50. Blackwell, T. K. and Weintraub, H. (1990) Differences and similarities in DNA binding preferences of Myo-D and E2A protein complexes revealed by binding site selection.Science 250, 1104–1110.

    Article  PubMed  CAS  Google Scholar 

  51. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.Science 249, 505–510.

    Article  PubMed  CAS  Google Scholar 

  52. Taylor, I. A., Watts, D., and Kneale, G. G. (1993) Substrate recognition and Selectivity in the Type IC DNA modification methylase M.Eco R124I.Nucleic Acids Res. 21, 4929–4935.

    Article  PubMed  CAS  Google Scholar 

  53. Taylor, J. D., Ackroyd, A. J., and Halford, S. E. (1994) The gel shift assay for the analysis of DNA-protein interactions, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions. (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 263–280.

    Chapter  Google Scholar 

  54. Turner, G. P. and Kneale, G. G. (1993) Cloning, expression and in vitro characterisation of the M13 gene 5 protein.Biochim. Biophys. Acta 1173, 201–208.

    PubMed  CAS  Google Scholar 

  55. Carpenter, M. L. and Kneale, G. G. (1994) Analysis of DNA-protein interactions by intrinsic fluorescence, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions. (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 313–326.

    Chapter  Google Scholar 

  56. Schuck, P. and Minton, A. P. (1996) Kinetic analysis of biosensor data: elementary tests for self-consistency.TIBS 21, 458–460.

    PubMed  CAS  Google Scholar 

  57. Taylor, I. A. and Kneale, G. G. (1994) A competition assay for DNA binding using the fluorescence probe ANS, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 327–338.

    Chapter  Google Scholar 

  58. Carpenter, M. L. and Kneale, G. G. (1994) Circular dichroism and fluorescence analysis of the interaction of Pf1 gene 5 protein with poly(dT).J. Mol. Biol. 217, 681–689.

    Article  Google Scholar 

  59. Carpenter, M. L. and Kneale, G. G. (1994) Circular dichroism for the analysis of DNA-protein interactions, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions (Kneale, G. G. ed.), Humana, Totowa, NJ, pp. 339–346.

    Chapter  Google Scholar 

  60. Taylor, I. A., Davis, K. G., Watts, D., and Kneale, G. G. (1994) DNA binding induces a major structural transition in a type I methyltransferase.EMBO J. 13, 5772–5778.

    PubMed  CAS  Google Scholar 

  61. Webb, M., Taylor, I., Firman, K., and Kneale, G. G. (1995) Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis.J. Mol. Biol. 280, 181–190.

    Article  Google Scholar 

  62. Taylor, I., Webb, M., and Kneale, G. G. (1996) Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues in the specificity subunit that are critical for DNA binding.J. Mol. Biol. 258, 62–73.

    Article  PubMed  CAS  Google Scholar 

  63. Kneale, G. G. (ed.) (1994)Methods in Molecular Biology, Vol. 30: DNA-Protein Interactions. Humana, Totowa, NJ.

    Google Scholar 

  64. Busby, S., Kolb, A., and Minchin, S. (1994) Assays for transcription factor activity, inMethods in Molecular Biology, Vol. 30: DNA-Protein Interactions (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 397–411.

    Chapter  Google Scholar 

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  1. Division of Molecular and Cell Biology, School of Biological Science, University of Portsmouth, Portsmouth, PO1 2DT, UK

    Matthew J. Guille & G. Geoff Kneale

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Correspondence to G. Geoff Kneale.

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Guille, M.J., Kneale, G.G. Methods for the analysis of DNA-protein interactions. Mol Biotechnol 8, 35–52 (1997). https://doi.org/10.1007/BF02762338

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