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| Other Sizes |
| Targets |
5'-O-DMT-rU 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 during solid-phase synthesis. The compound is a nucleoside antimetabolite/analog.
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| ln Vitro |
The in vitro activity of 5'-O-DMT-rU 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 using thermal melting (Tm) analysis.
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| ln Vivo |
In vivo studies for 5'-O-DMT-rU 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 DMT protecting group is removed during RNA synthesis and deprotection. The final RNA oligonucleotide contains the natural uridine nucleoside.
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| Enzyme Assay |
For RNA oligonucleotide synthesis, 5'-O-DMT-rU 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 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-rU 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-rU are characterized for the RNA oligonucleotides incorporating this building block rather than the protected nucleoside itself. The compound has a molecular formula of C30H30N2O8 and a molecular weight of 546.57-546.6. It should be stored at 4°C, protected from light. In solvent, it is stable for 6 months at -80°C or 1 month at -20°C (protected from light). The compound is a nucleoside antimetabolite/analog targeting DNA/RNA synthesis.
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| Toxicity/Toxicokinetics |
5'-O-DMT-rU is a research compound intended for laboratory use only and is not approved for human therapeutic use. As a modified nucleoside, it is used in RNA synthesis for various research applications. The compound features DMT protection of the 5'-hydroxyl. Standard laboratory safety precautions should be followed when handling this compound. Storage at 4°C, protected from light, is recommended.
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| Additional Infomation |
5'-O-DMT-rU is a ribonucleoside phosphoramidite building block for RNA synthesis with molecular formula C30H30N2O8 and molecular weight 546.57-546.6. It features DMT protection of the 5'-hydroxyl and is used in the solid-phase synthesis of RNA oligonucleotides. The compound is a nucleoside antimetabolite/analog targeting DNA/RNA synthesis. It is for research use only and has not been approved for clinical applications. Storage at 4°C, protected from light, is recommended.
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| Molecular Formula |
C30H30N2O8
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|---|---|
| Molecular Weight |
546.57
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| Exact Mass |
546.2
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| CAS # |
81246-79-9
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| PubChem CID |
11763309
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| Appearance |
White to off-white solid powder
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| Density |
1.343±0.06 g/cm3(Predicted)
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| Melting Point |
111-112 °C(Solv: ethyl acetate (141-78-6))
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| LogP |
2.181
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
8
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| Rotatable Bond Count |
9
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| Heavy Atom Count |
40
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| Complexity |
868
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| Defined Atom Stereocenter Count |
4
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| SMILES |
COC1=CC=C(C=C1)C(C2=CC=CC=C2)(C3=CC=C(C=C3)OC)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CC(=O)NC5=O)O)O
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| InChi Key |
PCFSNQYXXACUHM-YULOIDQLSA-N
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| InChi Code |
InChI=1S/C30H30N2O8/c1-37-22-12-8-20(9-13-22)30(19-6-4-3-5-7-19,21-10-14-23(38-2)15-11-21)39-18-24-26(34)27(35)28(40-24)32-17-16-25(33)31-29(32)36/h3-17,24,26-28,34-35H,18H2,1-2H3,(H,31,33,36)/t24-,26-,27-,28-/m1/s1
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| Chemical Name |
1-[(2R,3R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3,4-dihydroxyoxolan-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 : 250 mg/mL (457.40 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (3.81 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 20.8 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: ≥ 2.08 mg/mL (3.81 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in 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 20.8 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. View More
Solubility in Formulation 3: ≥ 2.08 mg/mL (3.81 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.8296 mL | 9.1480 mL | 18.2959 mL | |
| 5 mM | 0.3659 mL | 1.8296 mL | 3.6592 mL | |
| 10 mM | 0.1830 mL | 0.9148 mL | 1.8296 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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