![Ac-rC Phosphoramidite (N-acetyl-5'-O-(4,4-dimethoxytrityl)-2'-O-[(tert-butyl)dimethylsilyl]cytidine- 3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite)](/upload/1124/hy-w042357.png)
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| Targets |
Ac-rC Phosphoramidite does not have a specific biological target itself but serves as a building block for RNA synthesis. When incorporated into RNA oligonucleotides, it allows for the creation of phosphorodithioate (PS2) modifications, which can enhance nuclease resistance and binding affinity. The resulting modified RNA oligonucleotides can target various biological molecules for therapeutic and research applications. The DMT and TBDMS groups provide protection during synthesis.
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| ln Vitro |
The in vitro activity of Ac-rC Phosphoramidite 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. The purity of the compound (≥98% mixture of diastereomers) and its suitability for automated RNA synthesis are assessed by HPLC analysis. The resulting PS2-modified RNA oligonucleotides are evaluated for their enhanced properties, such as nuclease resistance and target binding affinity.
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| ln Vivo |
In vivo studies for Ac-rC Phosphoramidite are typically conducted on the modified RNA oligonucleotides synthesized using this building block rather than the phosphoramidite 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 phosphorodithioate modifications can enhance metabolic stability, potentially improving their in vivo performance.
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| Enzyme Assay |
For RNA oligonucleotide synthesis, Ac-rC Phosphoramidite is dissolved in anhydrous acetonitrile and coupled to the growing oligonucleotide chain 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 TBDMS group is typically removed using fluoride-based reagents. The final PS2-modified 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 PS2-modified RNA oligonucleotides synthesized using Ac-rC Phosphoramidite. 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. The enhanced nuclease resistance of PS2-modified oligonucleotides is also assessed.
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| Animal Protocol |
For in vivo evaluation of modified 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 Ac-rC Phosphoramidite are characterized for the modified RNA oligonucleotides incorporating this building block. The compound has a molecular weight of 902.10 and a purity of ≥98% (mixture of diastereomers). It is typically handled as a solid and stored at -20°C under inert gas to maintain stability. Detailed PK parameters depend on the specific oligonucleotide sequence and the nature of the PS2 modifications.
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| Toxicity/Toxicokinetics |
The toxicity profile of Ac-rC Phosphoramidite is not explicitly detailed in the provided sources. As a chemical reagent, standard laboratory safety precautions should be followed when handling it. It is intended for research use only and is not for human therapeutic applications. The compound's safety would be evaluated in the context of the final oligonucleotide product rather than the phosphoramidite itself.
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| References | |
| Additional Infomation |
Ac-rC Phosphoramidite is a modified RNA phosphoramidite with a molecular formula of C47H64N5O9PSi and a molecular weight of 902.10. It is used for the synthesis of phosphorodithioate (PS2)-modified RNA oligonucleotides. It can also be used for inverse electron-demand Diels-Alder reactions for RNA labeling. This research compound is for laboratory use only and has not been approved for clinical applications.
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| Molecular Formula |
C47H64N5O9PSI
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| Molecular Weight |
902.10
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| Exact Mass |
901.421
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| CAS # |
121058-88-6
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| PubChem CID |
11814945
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| Appearance |
White to off-white solid powder
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| LogP |
10.84
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
11
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| Rotatable Bond Count |
21
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| Heavy Atom Count |
63
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| Complexity |
1560
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| Defined Atom Stereocenter Count |
4
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| SMILES |
CC(C)N(C(C)C)P(OCCC#N)O[C@@H]1[C@H](O[C@H]([C@@H]1O[Si](C)(C)C(C)(C)C)N2C=CC(=NC2=O)NC(=O)C)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC
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| InChi Key |
QKWKXYVKGFKODW-ZYRNLWDWSA-N
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| InChi Code |
InChI=1S/C47H64N5O9PSi/c1-32(2)52(33(3)4)62(58-30-16-28-48)60-42-40(59-44(43(42)61-63(11,12)46(6,7)8)51-29-27-41(49-34(5)53)50-45(51)54)31-57-47(35-17-14-13-15-18-35,36-19-23-38(55-9)24-20-36)37-21-25-39(56-10)26-22-37/h13-15,17-27,29,32-33,40,42-44H,16,30-31H2,1-12H3,(H,49,50,53,54)/t40-,42-,43-,44-,62?/m0/s1
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| Chemical Name |
N-[1-[(2S,3S,4S,5S)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]-3-[tert-butyl(dimethyl)silyl]oxy-4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyoxolan-2-yl]-2-oxopyrimidin-4-yl]acetamide
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| Synonyms |
Ac-rC Phosphoramidite
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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 (~110.9 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: 2.5 mg/mL (2.77 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 (2.77 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 | 1.1085 mL | 5.5426 mL | 11.0852 mL | |
| 5 mM | 0.2217 mL | 1.1085 mL | 2.2170 mL | |
| 10 mM | 0.1109 mL | 0.5543 mL | 1.1085 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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