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S1 Nuclease Protection Mapping

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Book cover Transgenesis Techniques

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 18))

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Abstract

The use of S1 nuclease to map the start site of a transcription unit is a well-established technique. Based on the method of Berk and Sharp (1), it has undergone many refinements over the years. S1 nuclease mapping requires a relatively detailed knowledge of the gene structure and sequence data (or a very good restriction map) of the first exon and several hundred bases of upstream sequence. Although S1 nuclease mapping is mainly used to map transcription start sites accurately (to be described in this chapter), this method can also be used to map intron-exon junctions (2). Note that in order to identify a transcriptional start site unambiguously, S1 nuclease mapping should be used in conjunction with primer extension (Chapter 44).

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References

  1. Berk, A. J. and Sharp, P. A. (1977) Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12,721–732.

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  2. Favaloro, J., Treisman, R., and Kamen, R. (1980) Transcription maps of polyoma virus-specific RNA: Analysis by two-dimensional nuclease S1 gel mapping. Methods in Enzymol. 65, 718–749.

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  3. Casey, J. and Davidson, N. (1977) Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplex at high concentrations of formamide. Nucleic Acids Res. 4, 1539.

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  4. Haywood, G. S. (1972) Gel electrophoretic separation of the complimentary strands of bacteriophage DNA. Virology 49, 342.

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  5. Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, vol. 2. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

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Author information

Authors and Affiliations

  1. Molecular Neurobiology Laboratory, Institute of Molecular and Cell Biology, National University of Singapore, Republic of Singapore

    Duncan R. Smith

Authors
  1. Duncan R. Smith
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Editor information

Editors and Affiliations

  1. National University of Singapore, Republic of Singapore

    David Murphy  & David A. Carter  & 

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© 1993 Humana Press Inc., Totowa, NJ

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Smith, D.R. (1993). S1 Nuclease Protection Mapping. In: Murphy, D., Carter, D.A. (eds) Transgenesis Techniques. Methods in Molecular Biology™, vol 18. Humana Press. https://doi.org/10.1385/0-89603-245-0:363

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  • DOI: https://doi.org/10.1385/0-89603-245-0:363

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-245-3

  • Online ISBN: 978-1-59259-505-1

  • eBook Packages: Springer Protocols

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