S1 nuclease is an endonuclease that specifically cleaves single-stranded nucleic acids. It is often used in molecular biology to:
Remove single-stranded overhangs: After certain restriction enzyme digestions, DNA fragments may have single-stranded "sticky ends." S1 nuclease can be used to trim these to create blunt ends.
Map gene transcripts: In a technique called S1 nuclease mapping, the enzyme is used to determine the start and end points of a gene transcript by digesting the single-stranded loops of a DNA-RNA hybrid.
Remove single-stranded DNA from a mixture: The enzyme can selectively remove single-stranded DNA or RNA from a sample containing both single- and double-stranded molecules.