5'-O-DMT-2'-O-TBDMS-N4-acetylcytidine
Oligonucleotide Synthesis, RNA Raw Materials & Modification
Product summary
Quick view
- Product family
- Oligonucleotide Synthesis, RNA Raw Materials & Modification
- MF
- C38H47N3O8Si
- MW
- 701.9
- Purity
- 99.80% (LC-MS)
5'-O-DMT-2'-O-TBDMS-N4-acetylcytidine is cytidine carrying three protecting groups: a 5'-O-(4,4'-dimethoxytrityl) (DMT) group, a 2'-O-(tert-butyldimethylsilyl) (TBDMS) group, and an N4-acetyl base-protecting group. CH64111 is identified by CAS 121058-85-3, molecular formula C38H47N3O8Si, molecular weight 701.9, PubChem CID 11136250, and InChIKey ZFRWPAYPCFTQHK-HYGOWAQNSA-N.
It is an RNA phosphoramidite precursor: the acid-labile 5'-DMT group is removed at the start of each chain-elongation cycle, the 2'-O-TBDMS group protects the ribose 2'-hydroxyl during RNA synthesis, and the N4-acetyl group masks the cytosine exocyclic amine and is removed at final deprotection.
Synonyms
5'-O-DMT-2'-O-TBDMS-N4-acetylcytidine; 5'-O-DMT-2'-O-tert-butyldimethylsilyl-N4-Ac-rC; DMT-2'-TBDMS-rC(Ac)
Identity and specifications
| Catalog No. | CH64111 |
| CAS No. | 121058-85-3 |
| Molecular Formula | C38H47N3O8Si |
| Molecular Weight | 701.9 |
| PubChem CID | 11136250 |
| InChIKey | ZFRWPAYPCFTQHK-HYGOWAQNSA-N |
| Purity | 99.80% (LC-MS) |
Storage conditions
2-8 C
Technical attributes
- Nucleobase
- Cytosine
- 5'-O protection
- DMT (dimethoxytrityl)
- 2'-O protection
- TBDMS (tert-butyldimethylsilyl)
- Base protection
- N4-Acetyl
- Packaging
- 100 mg; 500 mg; 1 g; 5 g; 1 mL; Custom packaging on request
- Solution concentration
- 10 mM in DMSO
- Water content
- <=1.0%
- Physical form
- white to off-white powder
- Stability
- User-prepared stock solution: 6 months at -80 C or 1 month at -20 C; protect from light
Application context
- 5'-DMT 5'-OH protection: the acid-labile 4,4'-dimethoxytrityl group protects the 5'-hydroxyl and is removed at the start of each RNA chain-elongation cycle.
- 2'-O-TBDMS 2'-OH protection: the tert-butyldimethylsilyl group protects the ribose 2'-hydroxyl during solid-phase RNA synthesis.
- N4-acetyl base protection: the acetyl group masks the cytosine exocyclic amine during synthesis and is removed at 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 11136250
PubChem · CID 11136250
Frequently Asked Questions
What do the three protecting groups on this cytidine do?
The 5'-O-DMT group is an acid-labile 5'-hydroxyl protection removed at the start of each RNA chain-elongation cycle; the 2'-O-TBDMS group protects the ribose 2'-hydroxyl during solid-phase RNA synthesis; and the N4-acetyl group protects the cytosine exocyclic amine, removed at final deprotection.
How does it differ from 5'-O-DMT-2'-O-TBDMS-N4-benzoylcytidine?
Both are 5'-O-DMT-2'-O-TBDMS-protected cytidines with a protected cytosine N4-amine, but this one uses an acetyl group rather than benzoyl. The benzoyl form is cataloged separately.
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