Common Applications for Exonucleases and Endonucleases

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  • 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.