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| Other Sizes |
| Targets |
5'-O-DMT-N4-Ac-2'-F-dC does not have a specific biological target itself but serves as a building block for oligonucleotide synthesis. When incorporated into oligonucleotides, the 2'-fluoro modification enhances nuclease resistance and increases binding affinity to complementary RNA targets. The resulting oligonucleotides 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.
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| ln Vitro |
The in vitro activity of 5'-O-DMT-N4-Ac-2'-F-dC is assessed by its utility as a building block in oligonucleotide 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 resulting 2'-fluoro-modified oligonucleotides are evaluated for their binding affinity to complementary RNA targets using thermal melting (Tm) analysis. Nuclease resistance is assessed by incubation with various nucleases followed by gel electrophoresis or HPLC analysis.
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| ln Vivo |
In vivo studies for 5'-O-DMT-N4-Ac-2'-F-dC are typically conducted on the modified oligonucleotides incorporating 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 siRNA. The 2'-fluoro modification enhances metabolic stability and reduces immunogenicity of therapeutic oligonucleotides, potentially improving their in vivo performance.
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| Enzyme Assay |
For oligonucleotide synthesis, 5'-O-DMT-N4-Ac-2'-F-dC is converted to the corresponding phosphoramidite and incorporated into oligonucleotides using standard solid-phase synthesis protocols. Coupling efficiency is monitored by trityl cation release measurements at each synthesis cycle. After synthesis, the oligonucleotide is cleaved from the solid support and deprotected using appropriate reagents. The acetyl protecting group is removed under mild deprotection conditions. The final oligonucleotide is purified by HPLC or PAGE and characterized by mass spectrometry.
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| Cell Assay |
For cellular uptake and activity studies, cultured cells are treated with modified oligonucleotides containing 5'-O-DMT-N4-Ac-2'-F-dC. 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 siRNA applications, target gene silencing is assessed at the mRNA and protein levels. Cytotoxicity is assessed using MTT or CellTiter-Glo assays.
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| Animal Protocol |
For in vivo evaluation of modified 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. The 2'-fluoro modification enhances metabolic stability of the oligonucleotides.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties of 5'-O-DMT-N4-Ac-2'-F-dC are typically characterized for the modified oligonucleotides incorporating this nucleoside. The 2'-fluoro modification increases metabolic stability by reducing susceptibility to nuclease degradation. The compound has a molecular formula of C32H32FN3O7 and a molecular weight of 589.61. It is typically handled as a solid and stored at -20°C under inert gas to maintain stability. The acetyl protecting group allows for milder deprotection conditions.
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| Toxicity/Toxicokinetics |
5'-O-DMT-N4-Ac-2'-F-dC 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 the synthesis of oligonucleotides with enhanced properties for therapeutic and research applications. The compound features DMT, acetyl, and 2'-fluoro modifications. 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-N4-Ac-2'-F-dC is a modified nucleoside building block for oligonucleotide synthesis with molecular formula C32H32FN3O7 and molecular weight 589.61. It features DMT protection of the 5'-hydroxyl, acetyl protection of the N4 position of cytosine, and a 2'-fluoro modification that enhances nuclease resistance and binding affinity. The compound is used in the synthesis of DNA or RNA oligonucleotides for therapeutic and research applications. It is for research use only and has not been approved for clinical applications.
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| Molecular Formula |
C32H32FN3O7
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|---|---|
| Molecular Weight |
589.61
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| Exact Mass |
589.222
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| CAS # |
159414-98-9
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| PubChem CID |
22094553
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| Appearance |
White to off-white solid powder
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| Density |
1.31±0.1 g/cm3(Predicted)
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| LogP |
3.897
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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 |
10
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| Heavy Atom Count |
43
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| Complexity |
994
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| Defined Atom Stereocenter Count |
4
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| SMILES |
CC(=O)NC1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC)O)F
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| InChi Key |
JIFNUYITABZZQS-PYYPWFDZSA-N
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| InChi Code |
InChI=1S/C32H32FN3O7/c1-20(37)34-27-17-18-36(31(39)35-27)30-28(33)29(38)26(43-30)19-42-32(21-7-5-4-6-8-21,22-9-13-24(40-2)14-10-22)23-11-15-25(41-3)16-12-23/h4-18,26,28-30,38H,19H2,1-3H3,(H,34,35,37,39)/t26-,28-,29-,30-/m1/s1
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| Chemical Name |
N-[1-[(2R,3R,4R,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3-fluoro-4-hydroxyoxolan-2-yl]-2-oxopyrimidin-4-yl]acetamide
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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 (424.01 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (3.53 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 (3.53 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 (3.53 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 | 1.6960 mL | 8.4802 mL | 16.9604 mL | |
| 5 mM | 0.3392 mL | 1.6960 mL | 3.3921 mL | |
| 10 mM | 0.1696 mL | 0.8480 mL | 1.6960 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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