Editing Enzyme Properties (section)

==== DNA Exonucleases ====

{| border="1" cellpadding="5" cellspacing="0"
|-
| Enzyme
| Substrate
| Activity
| Products
| Applications
| Heat Inactivationa
|-
| Exonuclease I,&nbsp;E. coli
| ssDNA
| 3´→5´ exonuclease
| dNMPs
| Removal of ssDNA and oligonucleotides.
| 15 min, 80°C
|-
| Exonuclease III,&nbsp;E. coli
| dsDNA
| 3´→5´ exonuclease that digests duplex DNA from the 3´ end of
a nick or a blunt or 3´-recessed end; not active on thionucleotides. Exo III also has 3´-DNA phosphatase and apurinic DNA endonuclease
activities.
| dNMPs and ssDNA on the opposite strand. Partial digestion produces dsDNA having 5´ extensions of ssDNA.
| Used with S1 Nuclease or Mung Bean Nuclease to make nested
deletions. Preparation of ssDNA templates for sequencing. Site-directed
mutagenesis. Preparation of labeled strand-specific probes.
| 20 min, 70°C
|-
| Exonuclease VII
| ssDNA
| Exonuclease that digests in both 5´→3´ and 3´→5´ directions.
| dNMPs
| Removal of primers and single-stranded oligos.
| 10 min, 95°C
|-
| Plasmid-Safe™ ATP-Dependent DNase
| linear ssDNA and dsDNA
| Selectively digests linear DNA. No activity on nicked or closed-circular DNA.
| dNMPs
| Remove chromosomal DNA fragments from plasmid, fosmid, and BAC preparations.
| NT
|-
| Lambda Exonuclease
| dsDNA
| 5´→3´ exonuclease that digests dsDNA from 5´-phosphorylated
blunt or recessed ends. It has low activity on 5´-hydroxyl ends and is
not active on nicked DNA.
| dNMPs and ssDNA on the opposite strand. Partial digestion produces dsDNA having 3´ extensions of ssDNA.
| Preparation of ssDNA templates for sequencing.
| 10 min, 75°C
|-
| RecBCD Nuclease,&nbsp;E. coli
| dsDNA and ssDNA
| An ATP- and Mg2+-dependent exonuclease that digests linear
DNA in both 5´→3´ and 3´→5´ directions. Not active on nicked or
closed-circular dsDNA.
| dNMPs
| Removal of linear DNA from circular DNA.
| NT
|-
| Rec J Exonuclease
| ssDNA
| 5´→3´ exonuclease that digests ssDNA with a 5´ phosphate or a 5´OH.
| dNMPs
| Removal of primers and ssDNA from dsDNA.
| 20 min, 65°C
|-
| T5 Exonuclease
| dsDNA and ssDNA
| 5´→3´ exonuclease that also has single-strand-specific
endonuclease activity in presence of 1-10 mM Mg2+&nbsp;ions. At <1 mM Mg2+, the 5´→3´ exonuclease can digest from a nick in
closed-circular dsDNA without digesting the opposite strand.
| dNMPs. Circular ssDNA is obtained from closed-circular dsDNA in presence of <1mM Mg2+.
| Plasmid mutagenesis. Oligonucleotide site-directed
mutagenesis. Removing linear DNA from plasmid preps. Preparation of
circular ssDNA
| NT
|}

{| border="1" cellpadding="5" cellspacing="0"
|-
| Exonuclease VII
| ssDNA
| Exonuclease that digests in both 5´→3´ and 3´→5´ directions.
| dNMPs
| Removal of primers and single-stranded oligos.
| 10 min, 95°C
|-
| Plasmid-Safe™ ATP-Dependent DNase
| linear ssDNA and dsDNA
| Selectively digests linear DNA. No activity on nicked or closed-circular DNA.
| dNMPs
| Remove chromosomal DNA fragments from plasmid, fosmid, and BAC preparations.
| NT
|-
| Lambda Exonuclease
| dsDNA
| 5´→3´ exonuclease that digests dsDNA from 5´-phosphorylated
blunt or recessed ends. It has low activity on 5´-hydroxyl ends and is
not active on nicked DNA.
| dNMPs and ssDNA on the opposite strand. Partial digestion produces dsDNA having 3´ extensions of ssDNA.
| Preparation of ssDNA templates for sequencing.
| 10 min, 75°C
|-
| RecBCD Nuclease,&nbsp;E. coli
| dsDNA and ssDNA
| An ATP- and Mg2+-dependent exonuclease that digests linear
DNA in both 5´→3´ and 3´→5´ directions. Not active on nicked or
closed-circular dsDNA.
| dNMPs
| Removal of linear DNA from circular DNA.
| NT
|-
| Rec J Exonuclease
| ssDNA
| 5´→3´ exonuclease that digests ssDNA with a 5´ phosphate or a 5´OH.
| dNMPs
| Removal of primers and ssDNA from dsDNA.
| 20 min, 65°C
|-
| T5 Exonuclease
| dsDNA and ssDNA
| 5´→3´ exonuclease that also has single-strand-specific
endonuclease activity in presence of 1-10 mM Mg2+&nbsp;ions. At <1 mM Mg2+, the 5´→3´ exonuclease can digest from a nick in
closed-circular dsDNA without digesting the opposite strand.
| dNMPs. Circular ssDNA is obtained from closed-circular dsDNA in presence of <1mM Mg2+.
| Plasmid mutagenesis. Oligonucleotide site-directed
mutagenesis. Removing linear DNA from plasmid preps. Preparation of
circular ssDNA
| NT
|}

a.&nbsp;NT, not tested.