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Properties of DNA Repair Enzymes and Structure-specific Endonucleases
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 | |
---|---|---|---|---|---|---|---|
5′ | 3′ | ||||||
APE 1 | AP site | 1st phosphodiester bond 5′ to AP site | 1nt 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 | P | 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 | 1nt gap | P | PA | Glycosylase & AP lyase | |
Tma Endo III | AP site, damaged pyrimidines, Tg | N-glycosidic bond; 1st phosphodiester bond 3′ to AP site | 1nt gap | P | PA | Glycosylase & AP lyase | YES |
Endo IV | AP site | 1st phosphodiester bond 5′ to AP site | 1nt gap | dR5P | OH | Endonuclease | |
Tth Endo IV | AP site | 1st phosphodiester bond 5′ to AP site | 1nt 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; 1nt gap | P6 | Glycosylase & AP lyase | ||
Endo VIII | AP site4 | phosphodiester bond 3′ & 5′ to AP site | 1nt 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; 1nt 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 |
1nt gap |
5'-P 3'-P | Glycosylase and AP lyase | No | |
THERMOLABILE USER II | dU | N-glycosidic bond; phosphodiester bond 3′ & 5′ to AP site |
1nt gap |
5'-P 3'-PA |
Glycosylase and AP lyase | No | |
THERMOLABILE USER III | dU | N-glycosidic bond; phosphodiester bond 3′ & 5′ to AP site |
1nt gap |
5'-dR5P 3'-OH |
Glycosylase and 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 | deoxyinosine |
dR5P | deoxyribose 5′-phosphate |
dU | deoxyuridine |
dX | deoxyxanthosine |
NA | Not applicable |
OH | Hydroxyl |
P | Phosphate |
PA | 3′-phospho-α, β-unsaturated aldehyde |
rN | ribonucleotides |
Tg | Thymine Glycol |
Footnotes
- activity is on dsDNA unless noted otherwise
- Minor activies, substrates, and references can be found at www.neb.com
- 5′ flaps of 1 - 40 nt in length have been confirmed substrates
- enzyme has robust activity on ssDNA in addition to dsDNA
- Antarctic Thermolabile UDG can be heat inactivated
- CPD still covalently attached