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| Other Sizes |
| Targets |
5-O-TBDMS-N4-Benzoyl-2-deoxycytidine does not have a specific biological target itself but serves as a protected cytidine building block for DNA synthesis. When incorporated into DNA oligonucleotides, the resulting sequences can target various biological molecules including mRNA (for antisense applications), DNA (for PCR and sequencing), or proteins (for aptamer applications). The TBDMS group provides 5'-hydroxyl protection, while the benzoyl group protects the N4 position of cytosine during synthesis.
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| ln Vitro |
The in vitro activity of 5-O-TBDMS-N4-Benzoyl-2-deoxycytidine is assessed by its utility as a building block in DNA synthesis. The efficiency of incorporation into growing oligonucleotide chains during solid-phase synthesis is evaluated by monitoring coupling efficiency. The purity of the compound (>98%+) and its suitability for automated DNA synthesis are assessed by HPLC analysis. The resulting DNA 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-TBDMS-N4-Benzoyl-2-deoxycytidine are typically conducted on the DNA 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 protecting groups (TBDMS and benzoyl) are removed during DNA synthesis and deprotection.
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| Enzyme Assay |
For DNA oligonucleotide synthesis, 5-O-TBDMS-N4-Benzoyl-2-deoxycytidine is converted to the corresponding phosphoramidite and incorporated into DNA oligonucleotides using standard solid-phase synthesis protocols. Coupling efficiency is monitored at each synthesis cycle. After synthesis, the oligonucleotide is cleaved from the solid support and deprotected using appropriate reagents. The TBDMS and benzoyl protecting groups are removed under standard deprotection conditions. The final DNA 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 DNA oligonucleotides synthesized using 5-O-TBDMS-N4-Benzoyl-2-deoxycytidine 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 DNA 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-TBDMS-N4-Benzoyl-2-deoxycytidine are characterized for the DNA oligonucleotides incorporating this building block rather than the protected nucleoside itself. The compound has a molecular formula of C22H31N3O5Si and a molecular weight of 445.58. Purity is 98%+. Appearance is white to off-white solid. Storage at 4°C, protected from light, is recommended. The TBDMS and benzoyl protecting groups provide orthogonal protection for selective deprotection.
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| Toxicity/Toxicokinetics |
5-O-TBDMS-N4-Benzoyl-2-deoxycytidine 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 DNA oligonucleotide synthesis for various research applications including gene regulation, diagnostics, and nucleic acid-based therapeutics. 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-TBDMS-N4-Benzoyl-2-deoxycytidine is a modified 2'-deoxycytidine nucleoside with molecular formula C22H31N3O5Si and molecular weight 445.58. It features TBDMS protection at the 5'-hydroxyl and benzoyl protection at the N4 amino group. The compound is used in the synthesis of modified DNA strands for gene regulation, diagnostics, and nucleic acid-based therapeutics. It is for research use only and has not been approved for clinical applications. Purity 98%+ and storage at 4°C, protected from light, is recommended.
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| Molecular Formula |
C22H31N3O5SI
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|---|---|
| Molecular Weight |
445.58
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| Exact Mass |
445.203
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| CAS # |
51549-36-1
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| PubChem CID |
14018201
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| Appearance |
White to off-white solid powder
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| LogP |
3.238
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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 |
7
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| Heavy Atom Count |
31
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| Complexity |
740
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| Defined Atom Stereocenter Count |
3
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| SMILES |
CC(C)(C)[Si](C)(C)OC[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=NC2=O)NC(=O)C3=CC=CC=C3)O
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| InChi Key |
CCPOWNJNXQQIFV-YQVWRLOYSA-N
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| InChi Code |
InChI=1S/C22H31N3O5Si/c1-22(2,3)31(4,5)29-14-17-16(26)13-19(30-17)25-12-11-18(24-21(25)28)23-20(27)15-9-7-6-8-10-15/h6-12,16-17,19,26H,13-14H2,1-5H3,(H,23,24,27,28)/t16-,17+,19+/m0/s1
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| Chemical Name |
N-[1-[(2R,4S,5R)-5-[[tert-butyl(dimethyl)silyl]oxymethyl]-4-hydroxyoxolan-2-yl]-2-oxopyrimidin-4-yl]benzamide
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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 (561.07 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (4.67 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 (4.67 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 (4.67 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 | 2.2443 mL | 11.2213 mL | 22.4427 mL | |
| 5 mM | 0.4489 mL | 2.2443 mL | 4.4885 mL | |
| 10 mM | 0.2244 mL | 1.1221 mL | 2.2443 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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