DNA Repair Enzymes on Damaged and Non-standard Bases
NEB carries an array of endonucleases and glycosylases for Base-excision repair (BER) for use in multiple applications. The following table indicates the level of repair on either double-stranded or single-stranded DNA oligos for various damaged and non-standard bases.
| Double-stranded DNA Oligos (34-mers) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| REPAIR ENZYME | AP:A | DHT:A | 5-hmU:A | 5-hmU:G | I:T | 6-MeA:T | 8-0G:C | 8-0G:G | U:A | U:G | X:G |
THYMINE GLYCOL:A |
| APE 1 | ++++ | + | - | - | - | - | - | - | - | - | - | - |
| Endo III | ++++ | + | - | - | - | - | - | - | - | - | - | - |
| Tma Endo III | ++++ | ++ | - | - | - | - | + | + | - | - | - | ++ |
| Endo IV | ++++ | + | - | - | - | - | - | - | - | - | - | - |
| Tth Endo IV | ++++ | + | - | - | - | - | - | + | - | - | - | - |
| Endo V* | +++ | + | + | + | ++++ | + | ++ | + | + | ++++ | - | ++ |
| T4 PDG | ++++ | - | - | - | - | - | - | - | - | - | - | - |
| Endo VIII | ++++ | ++ | - | - | - | - | - | - | - | - | - | ++++ |
| Thermostable EndoQ | +++ | - | - |
- |
+++ |
- |
- |
- |
++++ |
++++ |
++++ |
- |
| Fpg | + | + | - | - | - | - | ++++ | ++++ | - | - | - | + |
| hAAG | - | - | - | - | ++++ | - | - | - | - | - | - | - |
| hSMUG1 | N/A | - | +++ | +++ | - | - | - | - | ++++ | ++++ | - | - |
| Thermostable OGG** | - | - |
- | - | - | - | ++++ |
++++ |
- |
- | - | - |
| UDG | N/A | - | - | - | - | - | - | - | ++++ | + | - | - |
| Afu UDG | N/A | - | - | - | - | - | - | - | ++++ | + | - | - |
| Antarctic Thermolabile UDG | N/A | - | - | - | - | - | - | - | ++++ | + | - | - |
| WarmStart® Afu Uracil-DNA Glycosylase (UDG) |
N/A |
- |
- |
- |
- |
- |
- |
- |
++++ |
+ | - | - |
Standard reaction conditions were used to titer the enzymes with the alternate base
*Nicks only, does not remove damage
**Tested on 60-mer
| Single-stranded DNA Oligos (34-mers) | ||||||||
|---|---|---|---|---|---|---|---|---|
| REPAIR ENZYME | AP | DHT | 5-hmU | I | 6-MeA | 8-0G | U | X |
| APE 1 | ++ | - | - | - | - | - | - |
- |
| Endo III | ++ | - | - | - | - | - | - |
- |
| Tma Endo III | ++ | + | - | - | - | - | - |
- |
| Endo IV | - | - | - | - | - | - | - |
- |
| Tth Endo IV | - | - | - | - | - | - | - |
- |
| Endo V | + | - | - | ++++ | - | + | - |
- |
| T4 PDG | - | - | - | - | - | - | - |
- |
| Endo VIII | +++ | - | - | - | - | - | - |
- |
| Thermostable EndoQ | ++++ | - |
- |
++++ |
- |
- |
++++ |
++++ |
| Fpg | + | + | - | - | - | ++++ | - |
- |
| hAAG | - | - | - | + | - | - | - |
- |
| hSMUG1 | N/A | - | ++ | - | - | - | +++ |
- |
| Thermostable OGG | N/A | N/A | N/A | N/A | N/A | + | N/A |
N/A |
| UDG | N/A | - | - | - | - | - | ++++ |
- |
| Afu UDG | N/A | - | - | - | - | - | ++++ |
- |
| Antarctic Thermolabile UDG | N/A | - | - | - | - | - | ++++ |
- |
| WarmStart® Afu Uracil-DNA Glycosylase (UDG) |
N/A |
- |
- |
- |
- |
- |
++++ |
- |
Table Legend:
AP apurinic/apyrimidinic site. The AP site is created by treating a uracil containing oligo with UDG.
DHT 5,6-dihydrothymine
5-hmU 5-hydroxymethyluracil
I Inosine
6-MeA 6-methyladenine
8-OG 8-oxoguanine
U uridine
AP:A apurinic/apyrimidinic site base paired with adenine
DHT:A 5,6 dihydrothymine base paired with an adenine
5-hmU:A 5-hydroxymethyluracil base paired with an adenine
5-hmU:G 5-hydroxymethyluracil base paired with a guanine
I:T inosine base paired with a thymine
6-MeA:T 6-methyladenine base paired with a thymine
8-OG:C 8-oxoguanine base paired with a cytosine
8-OG:G 8-oxoguanine base paired with a guanine
NT: not tested
U:A uridine base paired with an adenine
U:G uridine base paired with a guanine
X: xanthine
X:G xanthine base paired with a guanine
Level of Repair:
++++100%
+++ 50%
++ 10% –25%
+ <10%
– no detectable enzyme activity (<0.7%) Some data were based on oligo data and visualization on a gel using ethidium bromide staining. Depending on the reaction conditions and sensitivity of detection, results may vary. Please be aware that star-activity (non-specific cleavage) may occur if enzyme is in excess.
N/A not applicable
