3'-O-TBDMS-Uridine CE Phosphoramidite
Oligonucleotide Synthesis, RNA Raw Materials & Modification
Product summary
Quick view
- Product family
- Oligonucleotide Synthesis, RNA Raw Materials & Modification
- MF
- C45H61N4O9PSi
- MW
- 861.0
- Purity
- >=98%
3'-O-TBDMS-Uridine CE Phosphoramidite is a regioisomeric RNA building block: 5'-O-(4,4'-dimethoxytrityl)-uridine with a 3'-O-(tert-butyldimethylsilyl) group and a 2'-O-(2-cyanoethyl N,N-diisopropyl)phosphoramidite group. CH65066 is identified by CAS 129451-77-0, molecular formula C45H61N4O9PSi, molecular weight 861.0, PubChem CID 14376044, and InChIKey UZVSHRLVIXPYEZ-ZMHKPELYSA-N.
Unlike the standard RNA amidite (2'-O-TBDMS, 3'-phosphoramidite), here the silyl group is on the 3'-hydroxyl and the phosphoramidite is on the 2'-hydroxyl. Coupling therefore forms 2'→5' internucleotide linkages. The acid-labile 5'-DMT is removed each cycle and the 3'-O-TBDMS protects the 3'-hydroxyl. Because uracil has no exocyclic amine, no base protecting group is required.
Synonyms
5'-O-DMT-3'-O-TBDMS-uridine 2'-CE phosphoramidite; 2'-phosphoramidite regioisomer
Identity and specifications
| Catalog No. | CH65066 |
| CAS No. | 129451-77-0 |
| Molecular Formula | C45H61N4O9PSi |
| Molecular Weight | 861.0 |
| PubChem CID | 14376044 |
| InChIKey | UZVSHRLVIXPYEZ-ZMHKPELYSA-N |
| Purity | >=98% |
Storage conditions
-20 +/- 5 C
Technical attributes
- Monomer class
- Regioisomeric RNA CE phosphoramidite
- Nucleobase
- Uracil
- 3'-O protection
- TBDMS
- Coupling position
- 2'-O phosphoramidite
- Packaging
- 50 mg; 100 mg; 250 mg; 1 g; 5 g; 25 g; Custom packaging on request
- Physical form
- white to light yellow powder
- Stability
- in solvent 6 months at -80 C; in solvent 1 month at -20 C
Application context
- 2'→5' linkage coupling monomer: the 2'-O-(2-cyanoethyl N,N-diisopropyl)phosphoramidite is the reactive coupling group, so internucleotide bonds form between the 2'-position and the next 5'-hydroxyl (2'→5' linkages).
- 5'-DMT + 3'-O-TBDMS protection: the acid-labile 5'-DMT is removed each cycle, while the 3'-O-TBDMS group protects the 3'-hydroxyl during synthesis.
- No base protection needed: uracil has no exocyclic amine, so this monomer requires no base protecting group.
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 14376044
PubChem · CID 14376044
Frequently Asked Questions
How does this differ from the standard 2'-O-TBDMS-rU amidite?
It is the regioisomer: the TBDMS group is on the 3'-hydroxyl and the phosphoramidite is on the 2'-hydroxyl (swapped versus the standard amidite). Coupling through the 2'-phosphoramidite forms 2'→5' internucleotide linkages instead of the usual 3'→5' linkages.
Why does the 3'-O-TBDMS-rU amidite have no base protecting group?
Uracil has no reactive exocyclic amine, so it needs no base protection. The monomer carries a 5'-O-DMT group (removed each cycle), a 3'-O-TBDMS group (protects the 3'-hydroxyl), and the 2'-phosphoramidite coupling group.
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