Properties of DNA Repair Enzymes and Structure-specific Endonucleases

NEB carries an array of reliable DNA repair enzymes for use in multiple applications.

Enzyme Major Substrate1,2 Cleave site Product(s) Produced Termini Created from Cleavage Major Activity Thermostable
           
APE 1  AP site 1st phosphodiester bond 5´ to AP site 1 nt gap dR5P  OH              Endonuclease  
Mismatch Endonuclease I
T:T, G:G and G:T Mismatches in dsDNA
3rd phosphodiester bond on the 5´ side of the mismatched base in both strands 
5 bp overhang OH Endonuclease
 
T7 Endo I  crucifroms, mismatches, Holliday junctions, across DNA nicks phosphodiester bond 5´ to structure nick P              OH  Endonuclease  
Endo III  AP site, damaged pyrimidines, Tg N-glycosidic bond; 1st phosphodiester bond 3´ to AP site 1 nt gap P PA Glycosylase & AP lyase  
Tma Endo III  AP site, damaged pyrimidines, Tg N-glycosidic bond; 1st phosphodiester bond 3´ to AP site  1 nt gap P PA Glycosylase & AP lyase YES
Endo IV  AP site 1st phosphodiester bond 5´ to AP site 1 nt gap dR5P  OH              Endonuclease  
Tth Endo IV  AP site 1st phosphodiester bond 5´ to AP site  1 nt gap dR5P  OH              Endonuclease YES
Endo V  dI4, dU, AP site 2nd phosphodiester bond 3´ to dI nick P              OH              Endonuclease  
T4 PDG  CPD, AP site N-glycosidic bond; phosphodiester bond 3´ to AP site AP site; 1 nt gap P6 
Glycosylase & AP lyase               
Endo VIII  AP site4 phosphodiester bond 3´ & 5´ to AP site 1 nt gap P P AP lyase  
Thermostable FEN1  5´ DNA flap3 phosphodiester bond at base of flap nick P              OH (on flap)  Endonuclease YES
Fpg  8-oxoG, oxidized purines N-glycosidic bond; phosphodiester bond 3´ & 5´ to AP site AP site; 1 nt gap P P Glycosylase & AP lyase  
hAAG  3mA, 7mG, dI, dX  N-glycosidic bond AP site N/A N/A Glycosylase  
hSMUG1  dU4, 5-hmU, 5-hoU, 5-fU N-glycosidic bond AP site N/A N/A Glycosylase  
RNaseHII              rN in dsDNA phosphodiester bond 5´ to ribo nick P              OH  Endonuclease  
UDG  dU4 N-glycosidic bond AP site N/A N/A Glycosylase  
Afu UDG  dU4 N-glycosidic bond AP site N/A N/A Glycosylase YES
Antarctic Thermolabile UDG5  dU4           N-glycosidic bond
AP site
N/A
N/A
Glycosylase  
USER Enzyme dU       N-glycosidic bond; phosphodiester bond 3´ & 5´ to AP site
1 nt gap
P
Glycosylase & AP lyase  
Thermolabile USER II dU         N-glycosidic bond; phosphodiester bond 3´ & 5´ to AP site
1 nt gap

PA
Glycosylase & AP lyase  
Thermostable USER III dU       N-glycosidic bond; phosphodiester bond 3´ & 5´ to AP site
1 nt gap
dR5P OH
Glycosylase & AP lyase  YES

 
Table Legend:
3mA 3-methyladenine
5-fU 5-formyluridine
5-hmU 5-hydroxymethyluridine
5-hoU 5-hydroxyuridine
7mG 7-methylguanine
8-oxoG 8-oxo-7,8-dihydroguanine
AP apurinic/apyrimidinic sites
CPDs Cyclobutane pyrimidine dimers
dI deoxyisine
dR5P deoxyribose 5´-phosphate
dU deoxyuridine
dX deoxyxanthosine
NA t applicable
OH Hydroxyl
P Phosphate
PA 3´-phospho-α, β-unsaturated aldehyde
rN ribonucleotides
Tg Thymine Glycol

Foottes

  1. activity is on dsDNA unless ted otherwise
  2. Mir activies, substrates, and references can be found at www.neb.com
  3. 5´ flaps of 1 - 40 nt in length have been confirmed substrates
  4. enzyme has robust activity on ssDNA in addition to dsDNA
  5. Antarctic Thermolabile UDG can be heat inactivated
  6. CPD still covalently attached