S1 Mapping Using Single-Stranded DNA Probes

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 ).