Practice question

S1 nuclease, purified from Aspergillus oryzae, is a single-strand specific endonuclease widely used in transcript analysis. It hydrolyzes phosphodiester bonds in single-stranded DNA and RNA, degrading unpaired regions. Double-stranded DNA with nicks, gaps, or loops also serves as substrate because local single-stranded character is exposed. It does not cleave fully base-paired duplexes. This property underpins S1 nuclease protection assay, where RNA-DNA hybrids are protected while unhybridized single-stranded tails are digested, allowing precise mapping of transcript termini and intron-exon boundaries accurately.