Preparations of RNA containing an mRNA of interest are hybridized to a complementary single-stranded DNA probe. At the end of the reaction period, nuclease S1 is used to degrade unhybridized regions of the probe, and the surviving DNA-RNA hybrids are then separated by gel electrophoresis and visualized by either autoradiography or Southern hybridization. The method can be used to quantify RNAs, to map the positions of introns and to identify the locations of 5′ and 3′ ends of mRNAs on cloned DNA templates1,2,3.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Berk, A.J. & Sharp, P.A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12, 721–732 (1977).
Calzone, F.J., Britten, R.J. & Davidson, E.H. Mapping of gene transcripts by nuclease protection assays and cDNA primer extension. Methods Enzymol. 152, 611–632 (1987).
Favaloro, J., Treisman, R. & Kamen, R. Transcription maps of polyoma virus-specific RNA: analysis by two-dimensional nuclease S1 gel mapping. Methods Enzymol. 65, 718–749 (1980).
Rights and permissions
About this article
Cite this article
Mapping RNA with nuclease S1. Nat Methods 2, 397–398 (2005). https://doi.org/10.1038/nmeth0505-397
Issue Date:
DOI: https://doi.org/10.1038/nmeth0505-397