stylized illustration representing Deoxyribonucleases (DNases)

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
Exonuclease VII
  • Bi-directional exonuclease activity with single-stranded specificity
  • Removal of ssDNA from nucleic acid mixtures
ssDNA3 3'→ 5'
5'→ 3'
  • Oligonucleotides
Exonuclease, T7 Gene 6
  • Controlled stepwise digestion of double-stranded DNA from the 5' termini
  • Generation ssDNA templates for sequencing or SNP analysis
dsDNA and RNA:DNA hybrids 5'→ 3'
  • Oligonucleotides
  • 5'-dNMPs
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.