| Size | Price | Stock | Qty |
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| 10mg |
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| 50mg |
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| 100mg |
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| 250mg |
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| 500mg |
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| Other Sizes |
| Targets |
5-Ethynyluridine targets newly synthesized RNA in cells. As a nucleoside analog, it is incorporated into RNA during transcription, but not into DNA. The ethynyl group provides a chemical handle for subsequent detection through click chemistry with azide-containing fluorophores or other probes. This allows for the visualization and quantification of RNA synthesis in proliferating cells. The compound is used to study changes in transcription and RNA turnover.
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| ln Vitro |
In vitro, 5-Ethynyluridine is used to label newly synthesized RNA in cell culture. Cells are incubated with the compound, which is taken up and incorporated into nascent RNA transcripts. The labeled RNA can then be detected by click chemistry conjugation with azide-modified fluorophores. The compound can be used to measure RNA synthesis in proliferating cells. It is soluble in water up to 50 mM and in DMSO up to 100 mM. 5-Ethynyluridine has been used to detect transcription in vitro.
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| ln Vivo |
5-Ethynyluridine (75 mM in PBS, 1 μl; intracerebellar injection) has been demonstrated to mark neurons in the central nervous system of mice [1]. The mouse central nervous system does not contain 5-ethynyluridine (330-750 μMol/g; i.p.), but it does mark nascent RNA in cells of many organs and tissues [1].
In vivo, 5-Ethynyluridine can be used to label newly synthesized RNA in living organisms. It has been used to study changes in transcription in vivo and for isolation and sequencing of nascent RNA from neuronal populations. In vivo 5-Ethynyluridine labelling has been used to detect reduced transcription in Purkinje cell degeneration mouse mutants. The compound can be administered to animals to label newly synthesized RNA in tissues for subsequent analysis. |
| Enzyme Assay |
In vitro experiments with 5-Ethynyluridine typically involve adding the compound to cell culture media at concentrations of 0.1-1 mM for 1-24 hours. The compound is soluble in water at up to 50 mM and in DMSO at up to 100 mM. After incubation, cells are fixed and permeabilized. The incorporated 5-EU is then detected using click chemistry: cells are incubated with an azide-modified fluorophore, copper catalyst, and a reducing agent. The click reaction covalently links the fluorophore to the ethynyl group of incorporated 5-EU. Fluorescence is then visualized by microscopy or flow cytometry.
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| Cell Assay |
In vitro cell-based assays using 5-Ethynyluridine are performed in various cell types to measure RNA synthesis. Cells are cultured in media containing 5-EU at concentrations of 0.1-1 mM for 1-24 hours. After labeling, cells are fixed, permeabilized, and subjected to click chemistry for detection. The fluorescence intensity is proportional to the amount of newly synthesized RNA. The assay can be used to study the effects of drugs or genetic manipulations on transcription rates. Cell viability should be assessed as prolonged exposure to 5-EU may affect cell health.
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| Animal Protocol |
In vivo animal experiments with 5-Ethynyluridine involve administering the compound to animals to label newly synthesized RNA in tissues. The compound can be administered intraperitoneally or intravenously at doses typically ranging from 50-200 mg/kg. After a labeling period (e.g., 1-4 hours), tissues are harvested, fixed, and processed for detection by click chemistry. The labeled RNA can be visualized in tissue sections or isolated for sequencing. The compound has been used to detect reduced transcription in Purkinje cell degeneration mouse mutants.
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| ADME/Pharmacokinetics |
5-Ethynyluridine has a molecular weight of 268.22 g/mol and the formula C11H12N2O6. The compound is a white to light yellow powder with a melting point of 190°C. It is soluble in water up to 50 mM and in DMSO up to 100 mM. For storage, the compound is kept at -20°C under inert gas, protected from air and heat. The compound has an XLogP3 value of -1.7, indicating high water solubility. Its purity is typically ≥95%.
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| Toxicity/Toxicokinetics |
Specific toxicological data for 5-Ethynyluridine are not extensively provided. However, it has been reported that in vivo 5-ethynyluridine labelling can itself induce neurodegeneration. As a research chemical, it is intended for laboratory use only and is not for human consumption. Standard laboratory safety precautions should be followed when handling this compound, including the use of gloves and eye protection. The compound should be handled in a well-ventilated area.
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| References |
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| Additional Infomation |
5-Ethynyluridine (CAS 69075-42-9) is a cell-permeable uridine analog used for labeling newly synthesized RNA. It is also known as 5-EU and has the molecular formula C11H12N2O6. The compound is a clickable form of uridine that undergoes azide-alkyne cycloaddition with azide-containing molecules. It is incorporated into cellular RNA, but not DNA, and has been used to detect transcription in vitro and in vivo. 5-Ethynyluridine can be used for isolation and sequencing of nascent RNA from neuronal populations in vivo. The compound is intended for research use only.
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| Molecular Formula |
C11H12N2O6
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|---|---|
| Molecular Weight |
268.2228
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| Exact Mass |
268.07
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| CAS # |
69075-42-9
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| PubChem CID |
14885960
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| Appearance |
White to off-white solid powder
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| LogP |
-1.7
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| Hydrogen Bond Donor Count |
4
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
3
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| Heavy Atom Count |
19
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| Complexity |
493
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| Defined Atom Stereocenter Count |
4
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| SMILES |
C#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
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| InChi Key |
QCWBIPKYTBFWHH-FDDDBJFASA-N
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| InChi Code |
InChI=1S/C11H12N2O6/c1-2-5-3-13(11(18)12-9(5)17)10-8(16)7(15)6(4-14)19-10/h1,3,6-8,10,14-16H,4H2,(H,12,17,18)/t6-,7-,8-,10-/m1/s1
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| Chemical Name |
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-ethynylpyrimidine-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 |
| 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 (~372.83 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 0.71 mg/mL (2.65 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 7.1 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: ≥ 0.71 mg/mL (2.65 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 7.1 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: ≥ 0.71 mg/mL (2.65 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 | 3.7283 mL | 18.6414 mL | 37.2828 mL | |
| 5 mM | 0.7457 mL | 3.7283 mL | 7.4566 mL | |
| 10 mM | 0.3728 mL | 1.8641 mL | 3.7283 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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