Home Resources Selection Charts Common Applications for Exonucleases and Endonucleases

Common Applications for Exonucleases and Endonucleases

Need help finding the right exonuclease for your experiments? Try Exo Selector

 

Application Recommended Enzyme(s) Notes
Removal of 3′ overhangs
5′ overhang Fill in Treatment
Removal of single-stranded primers for nested PCR reactions
Removal of primers post PCR prior to DNA sequencing or SNP detection
  • 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
Removal of primers with or without 3′ or 5′ terminal phosphorothioate bonds

Generating ssDNA from linear dsDNA:

  • If 5′ → 3′ polarity required
  • If 3′ → 5′ polarity required

 

  • 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
Site-directed mutagenesis
  • Removes nicked-strand DNA from 3′ to 5′
  • Removes nicked-strand DNA from 5′ to 3′
Nick-site extension
Degradation of denatured DNA from alkaline-based plasmid purification methods for improving DNA cloning
Removal of chromosomal/linear DNA in plasmid preparations
  • 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
  • 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
Removal of contaminated DNA from RNA samples
Removing gDNA prior to RT-qPCR
  
Degradation of DNA strand in DNA:RNA hybrid duplex
  
Removal of template DNA from IVT reactions
Conversion of single-stranded DNA or RNA to 5′-mononucleotides
Analysis of base composition, potential damage and modification of nucleic acids
Preparation of double-stranded DNA fragments with 5′-OH and 3′-phosphate
Degradation of nucleic acids (both DNA and RNA) in crude cell-free extracts
Preparation of rabbit reticulocyte
Chromatin Immunoprecipitation (ChIP) analysis
*GMP-grade available