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| Targets |
As a chemical reagent for RNA synthesis, 3'-TBDMS-Bz-rA Phosphoramidite does not have a defined biological target. Its purpose is to serve as a building block for incorporating adenosine residues into synthetic RNA sequences during solid-phase oligonucleotide synthesis. The TBDMS protection at the 3'-position and benzoyl protection at the exocyclic amine enable selective deprotection and ensure proper base-pairing fidelity in the final RNA product.
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| ln Vitro |
In cell-free biochemical systems, this phosphoramidite monomer is incorporated into RNA oligonucleotide sequences during solid-phase synthesis. The resulting synthetic RNA molecules can be used in various applications including structural studies, ribozyme engineering, aptamer development, siRNA therapeutics, and antisense oligonucleotide research. The 2'-hydroxyl group of the incorporated adenosine retains its native ribose configuration, preserving the biological activity and recognition properties of the RNA.
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| ln Vivo |
This compound does not exhibit direct cellular activity as it is a chemical synthesis reagent rather than a bioactive molecule. RNA oligonucleotides synthesized using this monomer can be delivered into cells for various functional studies. The TBDMS protecting groups are removed during post-synthetic deprotection, yielding fully functional RNA molecules capable of participating in cellular processes including translation, RNA interference, and gene regulation. Cellular uptake of synthetic RNA typically requires transfection reagents or conjugation to cell-penetrating peptides.
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| Enzyme Assay |
The standard procedure for incorporating this phosphoramidite involves solid-phase RNA synthesis using standard phosphoramidite chemistry. The monomer is dissolved in anhydrous acetonitrile at 0.1-0.2 M concentration and coupled to the growing RNA chain using activator solutions such as 5-benzylthio-1H-tetrazole or 5-ethylthio-1H-tetrazole. Coupling times for RNA phosphoramidites are typically extended to 5-10 minutes compared to DNA synthesis. Following chain assembly, the RNA oligonucleotide is deprotected using a two-step procedure: TBDMS groups are removed with fluoride treatment, and nucleobase protecting groups are removed with ammonium hydroxide or methylamine.
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| Cell Assay |
No cell-based experimental protocols are directly applicable to this phosphoramidite monomer as it is a chemical synthesis reagent. The RNA oligonucleotides produced using this monomer can be evaluated in cell culture to assess their biological activity. Typical experiments include transfection of siRNA or antisense oligonucleotides into mammalian cell lines at concentrations of 10-100 nM, followed by analysis of target gene knockdown by qRT-PCR or Western blotting, assessment of cellular phenotypic changes, and evaluation of off-target effects.
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| Animal Protocol |
3'-TBDMS-Bz-rA Phosphoramidite is not administered to animals as it is a chemical intermediate for RNA synthesis. RNA oligonucleotides synthesized using this monomer may be evaluated in animal models for therapeutic applications. Typical studies involve administration of chemically modified RNA oligonucleotides to mice or rats via intravenous, subcutaneous, or intraperitoneal routes at doses of 1-30 mg/kg. Pharmacodynamic endpoints include target gene silencing in tissues, biomarker modulation, and therapeutic efficacy in disease models over periods of days to weeks.
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| ADME/Pharmacokinetics |
As a chemical reagent, this compound does not have established pharmacokinetic properties. The pharmacokinetics of RNA oligonucleotides synthesized using this monomer depend on the overall length, sequence, and chemical modifications. RNA molecules are rapidly degraded by nucleases in biological fluids, with plasma half-lives typically ranging from minutes to hours. Chemical modifications such as phosphorothioate linkages and 2'-modifications are often incorporated to enhance stability. Biodistribution of RNA oligonucleotides is predominantly to liver, kidney, and spleen.
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| Toxicity/Toxicokinetics |
The compound is not intended for therapeutic use and lacks established toxicity profiles. Standard laboratory safety precautions should be followed when handling this chemical reagent. RNA oligonucleotides can exhibit sequence-dependent toxicities including immune stimulation via Toll-like receptors, hepatotoxicity, and nephrotoxicity. Maximum tolerated doses in animal models vary widely depending on the specific RNA sequence and chemical modifications, typically ranging from 5-50 mg/kg in rodents.
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| Additional Infomation |
3'-TBDMS-Bz-rA Phosphoramidite is a research-grade chemical supplied for RNA oligonucleotide synthesis applications. It is not an approved pharmaceutical and has no clinical trial history. The compound is typically stored at -20°C under argon or nitrogen to prevent moisture absorption and oxidation of the phosphoramidite. Purity specifications generally exceed 97% by HPLC analysis. This product is for research use only and is not intended for human or veterinary therapeutic applications.
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| Molecular Formula |
C53H66N7O8PSI
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|---|---|
| Molecular Weight |
988.19
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| Exact Mass |
987.447
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| CAS # |
129451-75-8
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| PubChem CID |
14376009
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| Appearance |
White to off-white solid powder
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| LogP |
13.07
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
13
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| Rotatable Bond Count |
22
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| Heavy Atom Count |
70
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| Complexity |
1630
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| Defined Atom Stereocenter Count |
4
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| SMILES |
CC(C)N(C(C)C)P(OCCC#N)O[C@@H]1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)NC(=O)C4=CC=CC=C4)COC(C5=CC=CC=C5)(C6=CC=C(C=C6)OC)C7=CC=C(C=C7)OC)O[Si](C)(C)C(C)(C)C
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| InChi Key |
HRYAQLIYKSXPET-RFMFGJHUSA-N
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| InChi Code |
InChI=1S/C53H66N7O8PSi/c1-36(2)60(37(3)4)69(65-32-18-31-54)67-47-46(68-70(10,11)52(5,6)7)44(66-51(47)59-35-57-45-48(55-34-56-49(45)59)58-50(61)38-19-14-12-15-20-38)33-64-53(39-21-16-13-17-22-39,40-23-27-42(62-8)28-24-40)41-25-29-43(63-9)30-26-41/h12-17,19-30,34-37,44,46-47,51H,18,32-33H2,1-11H3,(H,55,56,58,61)/t44-,46-,47-,51-,69?/m1/s1
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| Chemical Name |
N-[9-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-4-[tert-butyl(dimethyl)silyl]oxy-3-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]purin-6-yl]benzamide
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| Synonyms |
3'-TBDMS-Bz-rA Phosphoramidite; 3'-TBDMS-Bz-rA Phosphoramidite
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month Note: Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture. |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
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| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.0120 mL | 5.0598 mL | 10.1195 mL | |
| 5 mM | 0.2024 mL | 1.0120 mL | 2.0239 mL | |
| 10 mM | 0.1012 mL | 0.5060 mL | 1.0120 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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