Enzymes that hydrolyze phosphodiester bonds, used in various molecular biology applications.

Properties of deoxyribonucleases (DNases)

Nuclease Applications Substrate Specificity, polarity of cleavage Reaction products
DNase I, RNase-free

DNase I, RNase-free with MnCl2

DNase I, RNase-free, HC
  • Preparation of DNA-free RNA
  • Removal of template DNA following in vitro transcription
  • Preparation of DNA-free RNA prior to RT-PCR
  • DNA labeling by nick-translation
  • DNase foot printing
ssDNA1
dsDNA
DNA in RNA-DNA
hybrids
Sequence and base unspecific
  • 5’-dNMPs
  • 5’-oligonucleotides
Endonuclease IV, E. coli (Endo IV)
  • Studies of DNA damage and repair
  • Single cell electrophoresis
  • SNP analysis
AP DNA 5' to an abasic site, 3'→ 5' exonuclease
  • DNA with nicks 5' to AP sites
Endonuclease V, T. maritima (Endo V)
  • High-throughput methods for mutation research 
  • Studies of mutagenesis and DNA repair
  • Mismatch cleavage
  • Genotyping
Deaminated DNA Second phosphodiester bond 3' to the lesion
  • Nicked DNA2
Exonuclease I (Exo I)
  • PCR product clean-up
  • Removal of ssDNA from nucleic acid mixtures
ssDNA3 3'→ 5'
  • 5'-dNMPs
  • 5'-terminal dinucleotides
Exonuclease III (Exo III)
  • Creation of unidirectional deletions in DNA fragments
  • Generation of ssDNA for sequencing
  • Site-directed mutagenesis
  • Preparation of strand specific probes
dsDNA (with nicks,
blunt ends, 5’-overhangs)4
3'→ 5'
  • 5'-dNMPs
  • ssDNA
AP DNA 5' to an abasic site
  • DNA with nicks 5' to AP sites
RNA in
RNA-DNA hybrids
3'→ 5'
  • NMP's
DNA with 3’-phosphorylated
ends
N/A
  • 3'-OH ends of DNA
Lambda Exonuclease
  • Generation of ssPCR products for sequencing, SSCP analysis, rolling circle amplification
  • Producing ssDNA from dsDNA fragments
5'-phosphorylated
dsDNA5
5'→ 3'
  • 5'-dNMPs

1 - ssDNA is cleaved slower than dsDNA.

2 - when enzyme is in excess, complimentary strand is also nicked, generating a double-stranded break.

3 - does not cleave DNA chains with terminal 3'-phosphoryl or acetyl groups. Not suitable for removing 3'- overhang ends of dsDNA - this activity is greatly reduced.

4 - not active on 3'-overhang ends of DNA that are at least 4 base long or on phosphorothioate-linked nucleotides or ssDNA.

5 - selectively digests the 5'-phosphorylated strand of dsDNA. Exhibits greatly reduced activity on ssDNA and non-phosphorylated DNA; has limited activity at gaps in DNA and no activity at nicks.