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| Other Sizes |
| Targets |
5'-O-TBDMS-dT does not have a specific biological target as a therapeutic agent but serves as a protected nucleoside building block for DNA synthesis. The TBDMS protecting group at the 5'-position allows for selective deprotection and chain elongation during solid-phase oligonucleotide synthesis. When incorporated into oligonucleotides, the protected nucleoside contributes to the DNA sequence and structure. The compound is used as an intermediate in the synthesis of modified oligonucleotides for various research applications including antisense therapy and nucleic acid structural studies.
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| ln Vitro |
In vitro activity of 5'-O-TBDMS-dT 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 purity of the compound and its suitability for automated DNA synthesis are assessed by HPLC analysis. The resulting oligonucleotides are evaluated for their ability to hybridize to complementary sequences using thermal melting (Tm) analysis and for their biological activity in various assays depending on the specific application.
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| ln Vivo |
In vivo studies for 5'-O-TBDMS-dT are typically conducted on the 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 nucleic acid-based therapeutics. The TBDMS protecting group is removed during oligonucleotide synthesis and deprotection, so the final oligonucleotide contains the natural thymidine nucleoside without the protecting group.
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| Enzyme Assay |
For oligonucleotide synthesis, 5'-O-TBDMS-dT is converted to the corresponding phosphoramidite and incorporated into oligonucleotides using standard solid-phase synthesis protocols. The compound is dissolved in anhydrous acetonitrile and coupled to the growing oligonucleotide chain using standard coupling chemistry. 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 ammonium hydroxide or other appropriate reagents. The final 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 oligonucleotides synthesized using 5'-O-TBDMS-dT 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 to ensure the oligonucleotides are non-toxic to cells.
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| Animal Protocol |
For in vivo evaluation of oligonucleotides synthesized using 5'-O-TBDMS-dT, mice or rats are administered the oligonucleotides via intravenous, subcutaneous, or intraperitoneal injection. 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 (e.g., tumor xenografts for antisense therapy), with tumor volume or disease biomarkers monitored over time. Toxicity is assessed by monitoring body weight, organ histopathology, and serum chemistry.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties of 5'-O-TBDMS-dT are characterized for the oligonucleotides incorporating this nucleoside rather than the protected monomer itself. The compound is soluble in DMSO at 100 mg/mL (280.51 mM). The TBDMS protecting group is removed during oligonucleotide deprotection, so the final oligonucleotide contains the natural thymidine nucleoside. The compound is typically stored at -20°C to maintain stability. Detailed PK parameters depend on the specific oligonucleotide sequence, length, and backbone chemistry.
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| Toxicity/Toxicokinetics |
5'-O-TBDMS-dT is a research compound intended for laboratory use only and is not approved for human therapeutic use. As a protected nucleoside, it is used as an intermediate in oligonucleotide synthesis for various research applications including therapeutic development, molecular diagnostics, and nucleic acid structural studies. The compound should be handled with standard laboratory safety precautions. Toxicity studies are typically conducted on the complete oligonucleotides rather than the protected nucleoside monomer. The compound is stable when stored as recommended.
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| Additional Infomation |
5'-O-TBDMS-dT is a thymidine derivative with the primary 5'-hydroxyl group protected as a tert-butyldimethylsilyl (TBDMS) ether, with molecular formula C16H28N2O5Si and molecular weight 356.49. It is used as a protected nucleoside building block in oligonucleotide synthesis for therapeutic development, molecular diagnostics, and nucleic acid structural studies. The compound is soluble in DMSO at 100 mg/mL. It is for research use only and has not been approved for clinical applications. Storage at -20°C is recommended.
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| Molecular Formula |
C16H28N2O5SI
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|---|---|
| Molecular Weight |
356.49
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| Exact Mass |
356.177
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| CAS # |
40733-28-6
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| PubChem CID |
10251259
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| Appearance |
White to off-white solid powder
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| Density |
1.25g/cm3
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| Boiling Point |
497.4ºC at 760mmHg
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| Melting Point |
198ºC
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| Flash Point |
254.6ºC
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| LogP |
1.515
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
5
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| Rotatable Bond Count |
5
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| Heavy Atom Count |
24
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| Complexity |
555
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| Defined Atom Stereocenter Count |
3
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| SMILES |
CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[Si](C)(C)C(C)(C)C)O
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| InChi Key |
IJWIJLIIOKZJMS-YNEHKIRRSA-N
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| InChi Code |
InChI=1S/C16H28N2O5Si/c1-10-8-18(15(21)17-14(10)20)13-7-11(19)12(23-13)9-22-24(5,6)16(2,3)4/h8,11-13,19H,7,9H2,1-6H3,(H,17,20,21)/t11-,12+,13+/m0/s1
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| Chemical Name |
1-[(2R,4S,5R)-5-[[tert-butyl(dimethyl)silyl]oxymethyl]-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-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 (280.51 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (7.01 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 (7.01 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 25.0 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: ≥ 2.5 mg/mL (7.01 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 | 2.8051 mL | 14.0256 mL | 28.0513 mL | |
| 5 mM | 0.5610 mL | 2.8051 mL | 5.6103 mL | |
| 10 mM | 0.2805 mL | 1.4026 mL | 2.8051 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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