| Size | Price | Stock | Qty |
|---|---|---|---|
| 25g |
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| Other Sizes |
| Targets |
N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine does not have a specific biological target itself but serves as a protected cytidine building block for oligonucleotide synthesis. When incorporated into oligonucleotides, the resulting sequences can target various biological molecules. The DMT group provides 5'-hydroxyl protection for controlled chain elongation, while the benzoyl group protects the exocyclic amine of cytosine during synthesis. The compound has been used in the synthesis of oligodeoxynucleotides containing a 3'-S-phosphorothiolate (3'-PS) linkage.
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|---|---|
| ln Vitro |
In vitro activity of N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine 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. The purity of the compound (min. 99.0% by HPLC) 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. The compound can be used for probing enzyme-catalyzed cleavage processes in DNA.
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| ln Vivo |
In vivo studies for N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine 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 compound has been used as a research tool for anti-viral and anti-cancer studies. The protecting groups are removed during oligonucleotide synthesis and deprotection.
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| Enzyme Assay |
For oligonucleotide synthesis, N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine 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 final oligonucleotide is purified by HPLC or PAGE and characterized by mass spectrometry. Purity is min. 99.0% by HPLC.
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| Cell Assay |
For cellular studies, cultured cells are treated with oligonucleotides synthesized using N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-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 anti-viral and anti-cancer studies, appropriate assays are used to assess efficacy. Cytotoxicity is assessed using MTT or CellTiter-Glo assays.
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| Animal Protocol |
For in vivo evaluation of oligonucleotides synthesized using N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine, 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 (e.g., tumor xenografts for anti-cancer studies). Toxicity is assessed by monitoring body weight, organ histopathology, and serum chemistry.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties of N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine are characterized for the oligonucleotides incorporating this building block rather than the protected nucleoside itself. The compound is typically handled as a white to almost white powder to crystalline solid. Purity is min. 99.0% by HPLC. Detailed PK parameters depend on the specific oligonucleotide sequence, length, and backbone chemistry. Storage at -20°C under inert gas is recommended.
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| Toxicity/Toxicokinetics |
N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine is a research compound intended for laboratory use only and is not approved for human therapeutic use. As a cytidine nucleoside derivative, it serves as a building block in oligonucleotide synthesis. The compound has been used as a research tool for anti-viral and anti-cancer studies. Standard laboratory safety precautions should be followed when handling this compound. Purity min. 99.0% by HPLC. Storage at -20°C under inert gas is recommended.
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| References | |
| Additional Infomation |
N4-Benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine is a cytidine nucleoside derivative with molecular formula C37H35N3O7 and min. 99.0% purity by HPLC. It is a building block in oligodeoxyribonucleotide synthesis, featuring DMT protection at the 5'-position and benzoyl protection at the N4-position of cytosine. The compound is used in anti-viral and anti-cancer research and for probing enzyme-catalyzed cleavage in DNA. It is for research use only and has not been approved for clinical applications. Purity min. 99.0% by HPLC. Storage at -20°C under inert gas is recommended.
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| Molecular Formula |
C37H35N3O7
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|---|---|
| Molecular Weight |
633.69
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| Exact Mass |
633.248
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| CAS # |
67219-55-0
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| PubChem CID |
2724490
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| Appearance |
White to off-white solid powder
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| Density |
1.27 g/cm3
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| Melting Point |
119 °C
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| Index of Refraction |
58 ° (C=1, MeOH)
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| LogP |
5.242
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
7
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| Rotatable Bond Count |
11
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| Heavy Atom Count |
47
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| Complexity |
1080
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| Defined Atom Stereocenter Count |
3
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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[C@@H](O4)N5C=CC(=NC5=O)NC(=O)C6=CC=CC=C6)O
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| InChi Key |
MYSNCIZBPUPZMQ-VOTWKOMSSA-N
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| InChi Code |
InChI=1S/C37H35N3O7/c1-44-29-17-13-27(14-18-29)37(26-11-7-4-8-12-26,28-15-19-30(45-2)20-16-28)46-24-32-31(41)23-34(47-32)40-22-21-33(39-36(40)43)38-35(42)25-9-5-3-6-10-25/h3-22,31-32,34,41H,23-24H2,1-2H3,(H,38,39,42,43)/t31-,32+,34+/m0/s1
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| Chemical Name |
N-[1-[(2R,4S,5R)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-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 : 100 mg/mL (157.81 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: 2.5 mg/mL (3.95 mM) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), suspension solution; with sonication.
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 (3.95 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 | 1.5781 mL | 7.8903 mL | 15.7806 mL | |
| 5 mM | 0.3156 mL | 1.5781 mL | 3.1561 mL | |
| 10 mM | 0.1578 mL | 0.7890 mL | 1.5781 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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