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
Enzymes
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 THYMINE GLYCOL:A
APE 1 ++++ + - - - - - - - - -
Endo III ++++ + - - - - - - - - +
Tma Endo III ++++ ++ - - - - + + - - ++
Endo IV ++++ + - - - - - - - - -
Tth Endo IV ++++ + - - - - - + - - -
Endo V* +++ + + + ++++ + ++ + + ++++ ++
Endo VIII ++++ ++ - - - - - - - - +++
Fpg + + - - - - ++++ ++++ - - +
hAAG - - - - ++++ - - - - - -
hNEIL1 ++++ ++ - - - - + + - - ++
hOGG1 ++ - - - - - ++++ + - - -
T4 PDG ++++ - - - - - - - - - -
UDG N/A - - - - - - - ++++ + -
Afu UDG N/A - - - - - - - ++++ + -
hSMUG1 N/A - +++ +++ - - - - ++++ ++++ -

Standard reaction conditions were used to titer the enzymes with the alternate base
*Nicks only, does not remove damage

Single-stranded DNA Oligos (34-mers)
Repair
Enzymes
ENZYME AP DHT 5-hmU I 6-MeA 8-0G U THYMINE GLYCOL:A
APE 1 ++ - - - - - - -
Endo III ++ - - - - - - -
Tma Endo III ++ + - - - - - -
Endo IV - - - - - - - -
Tth Endo IV - - - - - - - -
Endo V + - - ++++ - + - -
Endo VIII +++ - - - - - - -
Fpg + + - - - + - +
hAAG - - - + - - - -
hNEIL1 + + - - - - - +
hOGG1 ++ - - - - + - -
T4 PDG - - - - - - - -
UDG N/A - - - - - ++++ -
Afu UDG N/A - - - - - ++++ -
hSMUG1 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
U:A uridine base paired with an adenine
U:G uridine base paired with a guanine

Level of Repair:
++++100%
+++ 50%
++ 10% –25%
+ <10%
– no detectable enzyme activity (<0.7%) 
N/A not applicable