2'-O-Propargyl-C (Ac) CE Phosphoramidite
Oligonucleotide Synthesis, RNA Raw Materials & Modification
Product summary
Quick view
- Product family
- Oligonucleotide Synthesis, RNA Raw Materials & Modification
- MF
- C44H52N5O9P
- MW
- 825.9
- Purity
- 98%
2'-O-Propargyl-C (Ac) CE Phosphoramidite is a click-handle RNA building block: 5'-O-(4,4'-dimethoxytrityl)-N4-acetyl-2'-O-(prop-2-yn-1-yl)cytidine 3'-O-(2-cyanoethyl N,N-diisopropyl)phosphoramidite. It is identified by CAS 1498305-51-3, molecular formula C44H52N5O9P, molecular weight 825.9, PubChem CID 170899159, and InChIKey JIMYWWYYWAHJAD-ZMHKPELYSA-N.
The 2'-O-propargyl group is a permanent 2'-O-ether that carries a terminal alkyne (C≡CH) — it is not a protecting group. That terminal alkyne is a "click" handle: oligonucleotides bearing a terminal alkyne can be labeled after synthesis by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) with azide-bearing reporters. The monomer couples through a standard 3'-phosphoramidite (3'→5' linkages), the 5'-DMT is removed each cycle, and the N4-acetyl base group is removed at final deprotection.
Synonyms
5'-O-DMT-N4-Ac-2'-O-propargylcytidine 3'-CE phosphoramidite; 2'-O-(2-propynyl)-cytidine amidite
Identity and specifications
| Catalog No. | CH65074 |
| CAS No. | 1498305-51-3 |
| Molecular Formula | C44H52N5O9P |
| Molecular Weight | 825.9 |
| PubChem CID | 170899159 |
| InChIKey | JIMYWWYYWAHJAD-ZMHKPELYSA-N |
| Purity | 98% |
Storage conditions
-20 C
Technical attributes
- Monomer class
- 2'-O-propargyl CE phosphoramidite
- Nucleobase
- Cytosine
- Conjugation handle
- Terminal alkyne
- Base protection
- N4-acetyl
- Packaging
- 100 mg; 250 mg; 500 mg; 1 g; 5 g; 10 g; 100 g; 1 kg; Custom packaging on request
- Physical form
- white, off-white to faint yellow powder
Application context
- Internal click handle: the 2'-O-propargyl ether places a terminal alkyne at the 2'-position for post-synthetic conjugation.
- CuAAC labeling: the terminal alkyne reacts with azide-bearing reporters (dyes, biotin, other tags) by the copper-catalyzed azide-alkyne cycloaddition (click chemistry).
- 3'→5' coupling monomer: the 3'-phosphoramidite couples to form 3'→5' linkages; the 5'-DMT is removed each cycle and the N4-acetyl base-protecting group is removed during final deprotection.
Related technical resources
Oligonucleotide Modification
Sugar, base, backbone, terminal, and conjugation modifications for ASO, siRNA, guide RNA, aptamer, and research or labeling oligo projects.
Oligonucleotide Synthesis
Support for modified monomers, supports, sulfurizing reagents, cap analogs, and related oligo synthesis inputs.
Public references
- Sustainability Challenges and Opportunities in Oligonucleotide Manufacturing
Journal of Organic Chemistry, 2021
Product-family technical context
- Solid-phase supports for oligonucleotide synthesis
Current Protocols in Nucleic Acid Chemistry, 2013
Product-family technical context
- Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis
Tetrahedron Letters, 1981
Product-family technical context
- Synthesis of deoxyoligonucleotides on a polymer support
Journal of the American Chemical Society, 1981
Product-family technical context
- PubChem Compound 170899159
PubChem · CID 170899159
Frequently Asked Questions
What does the 2'-O-propargyl group provide?
It is a permanent 2'-O-ether that carries a terminal alkyne. The alkyne is a 'click' handle: after synthesis, the oligonucleotide can be conjugated to azide-bearing reporters (dyes, biotin, etc.) by the copper-catalyzed azide-alkyne cycloaddition (CuAAC).
Why is the cytosine acetyl-protected?
The N4-acetyl group masks the cytosine exocyclic amine during synthesis and is removed at final deprotection. The 5'-DMT is removed each coupling cycle, while the 2'-O-propargyl ether stays on the finished oligonucleotide as the click handle.
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