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.
