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Functional Groups (for DNA)

 
Functional Groups
Position
 
5’
3’
int
Alkyne
 
X
 
Amino / Amino-dT
X
X
X
Azide / Azide-dT
X
X
X
DBCO / DBCO-dT
X
 
X
Hexynyl
X
 
 
Phosphate
X
X
 
Phosphorothioate (PTO)
 
 
X
Thiol
X
X
 

 

Alkyne

3'-Alkyne
 

The alkyne group is used for copper assisted cycloaddition click chemistry.

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

Amino / Amino-dT

A primary amino group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface. Amino modifiers can be positioned at the 5’-end with either a standard (C6) or longer (C12) spacer arm. Amino modifications can be positioned at the 3’-end. Internal amino modifications can be introduced using an amino-dT base.

 
Functional Group
Position
Synthesis Scale [µmol]
Purification
 
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Amino C6
5’
X X X X X X X
3’
X X X X X X X
Amino C6-dT
Int
 
X X O
 
X X
X = available/on stock
O = on request
 

Azide / Azide-dT

Microsynth's Azide modification uses an NHS Ester functional group to attach an azide moiety at the 5', 3' or any internal position in an oligo. This azide moiety may subsequently be used to attach alkyne modified groups through the click reaction. The internal version of this modification is attached to the oligo through a dT base. Incorporation of the internal version will add a dT nucleotide at that position. To avoid adding an extra nucleotide, replace an existing T nucleotide in your sequence with the required modification.

 
Functional Group
Position
Synthesis Scale [µmol]
Purification
 
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
Azide
5’
  X X O   X X
3’
  X X O   X X
Azide-dT
Int
 
X X O   X X
X = available/on stock
O = on request
 

DBCO / DBCO-dT

DBCO is a cyclooctyne-based modifier for copper free click.

 
Functional Group
Position
Synthesis Scale [µmol]
Purification
 
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
DBCO
5’
  X X O   X  
3’
             
DBCO-dT
Int
 
X X O   X  
X = available/on stock
O = on request
 

Hexynyl

Hexynyl
 

The 5' Hexynyl group is used for copper assisted cycloaddition click chemistry. Oligonucleotides prepared using 5'-Hexynyl Phosphoramidite are stable to standard deprotection conditions and exhibit a slightly increased retention time on RP HPLC.

 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
5'  
X
X
O  
X
X
X = available/on stock
O = on request
 

Phosphate

Phosphate
 

5’ Phosphorylation is needed if an oligo is used as a substrate for DNA ligase. 3’ Phosphorylation will inhibit degradation by some 3’-exonucleases and can be used to block extension by DNA polymerases.

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

Phosphorothioate (PTO)

PTO
 

The phosphorothioate (PTO) bond substitutes a sulfur atom for a non-bridging oxygen in the phosphate backbone of an oligo. This modification renders the internucleotide linkage resistant to nuclease degradation. Phosphorothioate bonds can be introduced between the last 3-5 nucleotides at the 5'- or 3'-end of the oligo to inhibit exonuclease degradation. Including phosphorothioate bonds throughout the entire oligo will help reduce attack by endonucleases as well.

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

Thiol

 
 
Functionalization of oligos for coupling to small molecules, peptides or surfaces. (5' C6-Thiol, 3' C3-Thiol).
 
Position
Synthesis Scale [µmol]
Purification
 
0.04
0.2
1.0
15
Des
HPLC
PAGE
5'  
X
X
X  
X
X
3'  
X
X
O  
X
X
X = available/on stock
O = on request