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DNA-Footprinting using Crude Embryonic Extracts from Xenopus laevis

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Molecular Methods in Developmental Biology

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 127))

Abstract

The interactions of trans-acting factors with cis-acting DNA elements have been a mainstay of molecular biology. With the emergence of new techniques, it is becoming easier to investigate how specific genes are regulated in differentiating cells. In 1978, Galas and Schmitz developed a modified employment of the enzyme deoxyribonuclease I (DNase I) that made it possible to map the DNA-binding site of a putative transcription factor (1). With the advent of Maxam and Gilbert sequencing, it also became apparent that chemical nucleases could be used to investigate the nature of protein-DNA interactions (2). Although these techniques are applicable to other types of DNA-binding proteins, we will specifically consider transcription factors.

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References

  1. Galas, J. G. and Schmitz, A. (1978) DNase I footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acid Res. 5, 3157.

    Article  PubMed  CAS  Google Scholar 

  2. Maxam, A. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65, 499–560.

    Article  PubMed  CAS  Google Scholar 

  3. Sigman, D. S. and Chen, C. B. (1990) Chemical nucleases: new reagents in molecular biology. Ann. Rev. Biochem. 59, 207–236.

    Article  PubMed  CAS  Google Scholar 

  4. Shaw, P. E. and Stewart, A. F. (1994) DNA-protein interactions, in Methods in Molecular Biology, vol. 30 (Kneale, G. G., ed.), Humana, Totowa, NJ, pp. 79–95.

    Google Scholar 

  5. Sigman, D. S., Graham, D. R., D’Aurora, V., and Stern, A. M. (1979) Oxygen-dependent cleavage of DNA by the 1,10-phenanthroline-cuprous complex. J. Biol. Chem. 254, 12,269–12,272.

    PubMed  CAS  Google Scholar 

  6. Dorn, A., Bollekens, J., Staub, A., Benoist, C., and Mathis, D. (1987) A multiplicity of CCAAT box binding proteins. Cell 50, 863–872.

    Article  PubMed  CAS  Google Scholar 

  7. Orford, R. L., Robinson, C., Haydon, J., Patient, R. K., and Guille, M. J. (1998) The maternal CCAAT box transcription factor which controls GATA-2 expression is novel, developmentally regulated and contains a dsRNA-binding subunit. Mol. Cell. Biol. 18, 5557–5566.

    PubMed  CAS  Google Scholar 

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© 1999 Humana Press Inc.

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Orford, R., Mernagh, D., Guille, M. (1999). DNA-Footprinting using Crude Embryonic Extracts from Xenopus laevis . In: Guille, M. (eds) Molecular Methods in Developmental Biology. Methods in Molecular Biology™, vol 127. Humana Press. https://doi.org/10.1385/1-59259-678-9:187

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  • DOI: https://doi.org/10.1385/1-59259-678-9:187

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-790-8

  • Online ISBN: 978-1-59259-678-2

  • eBook Packages: Springer Protocols

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