Nuclease S1 is an endonuclease that is active against single-stranded DNA and RNA molecules. Although its primary substrate is single-stranded, it can also introduce single-stranded breaks in double-stranded DNA-RNA or DNA-RNA hybrids. Nuclease S1 is used in the laboratory as a reagent in nuclease protection assays. It is used in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA.