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| Other Sizes |
| Targets |
5'-O-DMT-2'-TBDMS-Uridine does not have a specific biological target itself but serves as a protected uridine building block for RNA synthesis. When incorporated into RNA oligonucleotides, the resulting sequences can target various biological molecules including mRNA (for antisense applications), viral RNA (for antiviral therapeutics), or proteins (for aptamer applications). The DMT group provides 5'-hydroxyl protection for controlled chain elongation, while the TBDMS group protects the 2'-hydroxyl during synthesis.
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|---|---|
| ln Vitro |
The in vitro activity of 5'-O-DMT-2'-TBDMS-Uridine is assessed by its utility as a building block in RNA synthesis. The efficiency of incorporation into growing oligonucleotide chains during solid-phase synthesis is evaluated by monitoring coupling efficiency through trityl cation release measurements. The purity of the compound and its suitability for automated RNA synthesis are assessed by HPLC analysis. The resulting RNA oligonucleotides are evaluated for their ability to hybridize to complementary sequences.
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| ln Vivo |
In vivo studies for 5'-O-DMT-2'-TBDMS-Uridine are typically conducted on the RNA oligonucleotides synthesized using this building block rather than the protected nucleoside itself. These oligonucleotides are evaluated in animal models for their pharmacokinetic properties, biodistribution, and therapeutic efficacy in applications such as antisense therapy or RNA-based therapeutics. The protecting groups are removed during RNA synthesis and deprotection.
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| Enzyme Assay |
For RNA oligonucleotide synthesis, 5'-O-DMT-2'-TBDMS-Uridine is converted to the corresponding phosphoramidite and incorporated into RNA oligonucleotides using standard solid-phase synthesis protocols. Coupling efficiency is monitored by trityl cation release measurements at each synthesis cycle. After synthesis, the RNA oligonucleotide is cleaved from the solid support and deprotected using appropriate reagents. The TBDMS group is typically removed using fluoride-based reagents such as TBAF. The final RNA oligonucleotide is purified by HPLC or PAGE and characterized by mass spectrometry.
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| Cell Assay |
For cellular studies, cultured cells are treated with RNA oligonucleotides synthesized using 5'-O-DMT-2'-TBDMS-Uridine as a building block. Cells are incubated with oligonucleotides for 24-72 hours, and cellular uptake is assessed by fluorescence microscopy or flow cytometry using fluorescently labeled oligonucleotides. For antisense applications, gene knockdown efficiency is evaluated by qRT-PCR or Western blot. For aptamer applications, binding to target proteins is assessed by surface plasmon resonance or ELISA. Cytotoxicity is assessed using MTT or CellTiter-Glo assays.
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| Animal Protocol |
For in vivo evaluation of RNA oligonucleotides, mice or rats are administered the oligonucleotides via various routes. Pharmacokinetic parameters including half-life, clearance, and tissue distribution are determined by measuring oligonucleotide concentrations in plasma and tissues using hybridization-based assays or LC-MS. For therapeutic applications, efficacy is evaluated in appropriate disease models, with disease biomarkers or survival monitored over time.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties of 5'-O-DMT-2'-TBDMS-Uridine are characterized for the RNA oligonucleotides incorporating this building block rather than the protected nucleoside itself. The compound is typically handled as a solid and stored at -20°C under inert gas to maintain stability. The TBDMS protecting group enables selective RNA synthesis by protecting the 2'-hydroxyl.
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| Toxicity/Toxicokinetics |
5'-O-DMT-2'-TBDMS-Uridine is a research compound intended for laboratory use only and is not approved for human therapeutic use. As a protected uridine building block, it is used in RNA oligonucleotide synthesis for various research applications. Standard laboratory safety precautions should be followed when handling this compound. Storage at -20°C under inert gas is recommended.
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| Additional Infomation |
5'-O-DMT-2'-TBDMS-Uridine is a protected uridine building block for RNA synthesis, featuring DMT protection of the 5'-hydroxyl and TBDMS protection of the 2'-hydroxyl for selective RNA synthesis. It is used in the synthesis of RNA oligonucleotides for therapeutic and research applications. The compound is for research use only and has not been approved for clinical applications.
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| Molecular Formula |
C36H44N2O8SI
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|---|---|
| Molecular Weight |
660.83
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| Exact Mass |
660.287
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| CAS # |
81246-80-2
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| PubChem CID |
11017778
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| Appearance |
White to light yellow solid powder
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| LogP |
5.211
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
8
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| Rotatable Bond Count |
12
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| Heavy Atom Count |
47
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| Complexity |
1070
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| Defined Atom Stereocenter Count |
4
|
| SMILES |
CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC)O
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| InChi Key |
KVHQIELPHWJPSY-WXQJYUTRSA-N
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| InChi Code |
InChI=1S/C36H44N2O8Si/c1-35(2,3)47(6,7)46-32-31(40)29(45-33(32)38-22-21-30(39)37-34(38)41)23-44-36(24-11-9-8-10-12-24,25-13-17-27(42-4)18-14-25)26-15-19-28(43-5)20-16-26/h8-22,29,31-33,40H,23H2,1-7H3,(H,37,39,41)/t29-,31-,32-,33-/m1/s1
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| Chemical Name |
1-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3-[tert-butyl(dimethyl)silyl]oxy-4-hydroxyoxolan-2-yl]pyrimidine-2,4-dione
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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: This product requires protection from light (avoid light exposure) during transportation and storage. |
| 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 Vitro) |
DMSO : 100 mg/mL (151.32 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (3.78 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 2.5 mg/mL (3.78 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.5132 mL | 7.5662 mL | 15.1325 mL | |
| 5 mM | 0.3026 mL | 1.5132 mL | 3.0265 mL | |
| 10 mM | 0.1513 mL | 0.7566 mL | 1.5132 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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