Home Tools & Resources Selection Charts Common Applications for Exonucleases and Endonucleases

Common Applications for Exonucleases and Endonucleases

Application	Recommended Enzyme(s)	Notes
Removal of 3′ overhangs	Quick Blunting Kit
5′ overhang Fill in Treatment	Quick Blunting Kit
Removal of single-stranded primers for nested PCR reactions	Thermolabile Exonuclease I
Removal of primers post PCR prior to DNA sequencing or SNP detection	Exonuclease I Thermolabile Exonuclease I Exonuclease VII MszExonuclease I	Quick Heat inactivation versus Exonuclease I For 3′ chemically modified primers Quick Heat inactivation versus Exonuclease I for 3′chemically modified primers
Mapping positions of introns in genomic DNA	Exonuclease VII
Removal of primers with or without 3′ or 5′ terminal phosphorothioate bonds	Exonuclease VII
Generating ssDNA from linear dsDNA: If 5′ → 3′ polarity required If 3′ → 5′ polarity required	Lambda Exonuclease Exonuclease III	Strand targeted for removal requires one 5′ end with phosphate Strand targeted for removal requires a 5′ overhang, a blunt end, or a 3′ overhang (with less than 4 bases)
Preparation of nested deletions in double-stranded DNA	Exonuclease III (E. coli) plus Exonuclease VII
Site-directed mutagenesis	Exonuclease III (E. coli) T7 Exonuclease	Removes nicked-strand DNA from 3′ to 5′ Removes nicked-strand DNA from 5′ to 3′
Nick-site extension	T7 Exonuclease
Degradation of denatured DNA from alkaline-based plasmid purification methods for improving DNA cloning	T5 Exonuclease
Removal of chromosomal/linear DNA in plasmid preparations	T5 Exonuclease Exonuclease V (RecBCD)	Degrades linear ss + dsDNA, nicked DNA Degrades linear ss + dsDNA: PREFERRED as Exo V will save nicked plasmids resulting in higher yields especially for low-copy number plasmid prep
Removal of unligated products (linear dsDNA) from ligated circular double-stranded DNA	T5 Exonuclease Exonuclease V (RecBCD)	Only the un-nicked form of ligated circular double-stranded remains Both nicked and unnicked-form of ligated circular double-stranded DNA remains
Removal of residual gDNA after purification of low copy plasmid	Exonuclease V (RecBCD)
Removal of contaminated DNA from RNA samples	DNase I DNase I-XT
Removal of template DNA from IVT reactions	DNase I-XT
Conversion of single-stranded DNA or RNA to 5′-mononucleotides	Nuclease P1
Analysis of base composition, potential damage and modification of nucleic acids	Nuclease P1
Preparation of double-stranded DNA fragments with 5′-OH and 3′-phosphate	Micrococcal Nuclease
Degradation of nucleic acids (both DNA and RNA) in crude cell-free extracts	Micrococcal Nuclease
Preparation of rabbit reticulocyte	Micrococcal Nuclease
Chromatin Immunoprecipitation (ChIP) analysis	Micrococcal Nuclease

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