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Nucleobase Modifications (for DNA)

 
Nucleobase Modifications Position
  5’ 3’ int
2’-Deoxyinosine (INO)   X X
2-Aminopurine     X
5-Me-dC     X
5-OH-Me-dC     X
Deoxyuridine     X
Mixed Bases     X
N6-Me-dA     X
Propynyl-dC     X
Propynyl-dU     X
TIPS-Alkyne-(C8)-dT O O O
TMS-Alkyne-(C8)-dT O O O

 

2’-Deoxyinosine (INO)

2’-Deoxyinosine (INO)
 

Historically, the first universal base employed was 2’-deoxyInosine (dI). DeoxyInosine is a naturally occurring base that, while not truly universal, is less destabilizing than mismatches involving the four standard bases. Hydrogen bond interactions between dI and dA, dG, dC and dT are weak and unequal, with the result that some base-pairing bias does exist with dI:dC > dI:dA > dI:dG > dI:dT. When present in a DNA template, deoxyInosine preferentially directs incorporation of dC in the growing nascent strand by DNA polymerase.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
3'  
X
X
O  
X
X
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

2-Aminopurine

2-Aminopurine
 

2-Aminopurine can substitute for dA in an oligonucleotide. It is a naturally fluorescent base that is sensitive to the local environment making it a useful probe for monitoring the structure and dynamics of DNA hairpins and for detecting the base stacking state of a duplex. 2-Aminopurine can be destabilizing and slightly lower the Tm.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

5-Methyl-2'-deoxycytidine

5-Me-dC
 

5-Methyl-2'-deoxycytidine when substituted for dC will increase the Tm by as much as 0.5°C per insertion. In addition, the presence of 5-Methyl dC in CpG motifs can prevent or limit unwanted immune responses that otherwise occur if oligos are administered in vivo, which is of particular importance in antisense applications.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

5-Hydroxmethyl dC

5-Hydroxmethyl dC
 

Hydroxmethyl dC is a recently discovered modified base with a probable epigenetic role.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

Deoxyuridine

2-Deoxyuridine
 

DNA analogue of RNA-U.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

Mixed Bases

Mixed Bases
 
 
Modification used for site-specific randomization.
 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

N6-Me-dA

N6-Me-dA
 
 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

Propynyl-dC

Propynyl-dC
 

Substitution of propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance base pairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: propynyl-dC 2.8°C per substitution; propynyl-dU 1.7°C per substitution.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

Propynyl-dU

Propynyl-dU
 

Substitution of propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance base pairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: propynyl-dC 2.8°C per substitution; propynyl-dU 1.7°C per substitution.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int  
X
X
O  
X
X
X = available/on stock
O = on request
 

TIPS-Alkyne-(C8)-dT

TIPS-Alkyne-dT
 

Click chemistry.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int   O O O   O O
X = available/on stock
O = on request
 

TMS-Alkyne-(C8)-dT

TMS-Alkyne-(C8)-dT
 

Click chemistry.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Int   O O O   O O
X = available/on stock
O = on request