Common Applications for Exonucleases and Endonucleases

Application	Recommended Enzyme(s)
Removal of 3′ overhangs	Quick Blunting Kit T4 DNA Polymerase* + dNTPs
5′ overhang Fill in Treatment	Quick Blunting Kit T4 DNA Polymerase* + dNTPs Klenow + dNTPs
Removal of oligonucleotides post PCR	Exonuclease I
Removal of Chromosomal DNA in plasmid preparations	Lambda Exonuclease (Exonuclease I can be added to remove ssDNA generated by Lambda Exonuclease) T5 Exonuclease (Degrades linear ss + dsDNA, nicked DNA) Exonuclease V (RecBCD) (Degrades linear ss + dsDNA)
Removal of DNA in RNA preparations	DNase I
Chromatin Immunoprecipitation (ChIP) analysis	Micrococcal Nuclease
Generating ssDNA from linear dsDNA If 5′ → 3′ polarity required (require one 5’-end with phosphate) If 3′ → 5′ polarity required (require one end with 5’ overhang and one end with 3’overhang) Best general choice	Lambda Exonuclease Exonuclease III Lambda Exonuclease

* T4 DNA Polymerase has a strong exo- activity.

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