S1 Mapping Using Single-Stranded DNA Probes

  • Stéphane Viville
  • Roberto Mantovani
Part of the Springer Protocols Handbooks book series (SPH)


The S1 nuclease is an endonuclease isolated from Aspergillus oryzae that digests single- but not double-stranded nucleic acid. In addition, it digests partially mismatched double-stranded molecules with such sensitivity that even a single base-pair mismatch can be cut and hence detected. In practice, a probe of end-labeled double-stranded DNA is denatured and hybridized to complementary RNA molecules. S1 is used to recognize and cut mismatches or unannealed regions and the products are analyzed on a denaturing polyacrylamide gel. A number of different uses of the S1 nuclease have been developed to analyze mRNA taking advantage of this property (1,2). Both qualitative and quantitative information can be obtained in the same experiment (3).


Aspergillus Oryzae Kinase Buffer 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 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.PubMedCrossRefGoogle Scholar
  2. 2.
    Favaloro, J., Treisman, R., and Kamen, R. (1980) Transcription maps of polyoma virus-specific RNA: analysis by two-dimensional nuclease S1 gel mapping. Meth. Enzymol. 65, 718–749.PubMedCrossRefGoogle Scholar
  3. 3.
    Weaver, R. F. and Weissmann, C. (1979) Mapping of RNA by a modification of Berk-Sharp procedure: the 5′ termini of 15 S β-globin mRNA precursor and mature 10 S β-globin mRNA have identical map coordinates. Nucleic Acids Res. 7, 1175–1193.PubMedCrossRefGoogle Scholar
  4. 4.
    Lopata, M. A., Sollner-Webb, B., and Cleveland, D. W. (1985) Surprising S1-resistant trimolecular hybrids: potential complication in interpretation of S1 mapping analysis. Mol Cell Biol. 5, 2842–2846.PubMedGoogle Scholar
  5. 5.
    Viville, S., Jongeneel, V., Koch, W., Mantovani, R., Benoist, C, and Mathis, D. (1991) The Ea promoter: a linker-scanning analysis. J. Immunol. 146, 3211–3217.PubMedGoogle Scholar
  6. 6.
    Dean, M. (1987) Determining the hybridization temperature for S1 nuclease mapping. Nucleic Acids Res. 15, 6754.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2000

Authors and Affiliations

  • Stéphane Viville
    • 1
  • Roberto Mantovani
    • 2
  1. 1.Institut de Genetique et de Biologie Moleculaire et CellulaireCNRS/INSERM/ULPStrasbourgFrance
  2. 2.Departimento de Genetica e di Biologia dei MicrorganismiUniversita de MilanoMilanItaly

Personalised recommendations