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| 1mg |
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| 5mg |
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| Targets |
CY5-N3 is a labeling reagent that reacts with alkyne-containing molecules via a copper-catalyzed azide-alkyne cycloaddition (CuAAC) or strain-promoted azide-alkyne cycloaddition (SPAAC) click reaction. This allows for the covalent attachment of the fluorescent dye to a wide variety of biomolecules, including proteins, nucleic acids, and carbohydrates.
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| ln Vitro |
In vitro, CY5-N3 is used for cell imaging through click reactions. It can be used to label biomolecules in live or fixed cells. Its far-red fluorescence minimizes background autofluorescence, making it ideal for high-sensitivity imaging applications. It is cell membrane permeable and can be used for live cell imaging.
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| ln Vivo |
In vivo, CY5-N3 is used for cell, tissue, and in vivo imaging. Its near-infrared fluorescence signal has low background and strong tissue penetration, making it suitable for deep-tissue molecular labeling and in vivo fluorescence imaging. It can be used to track biomolecules, study biodistribution, and monitor biological processes in live animals.
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| Enzyme Assay |
In vitro labeling with CY5-N3 is typically performed by reacting the azide-containing dye with an alkyne-modified biomolecule. The reaction is carried out in a suitable buffer, often at room temperature or 37°C, for 1-4 hours. The efficiency of the conjugation is monitored by techniques such as SDS-PAGE, HPLC, or mass spectrometry.
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| Cell Assay |
Cellular assays with CY5-N3 typically involve labeling cells with the dye via click chemistry. Cells are first incubated with a molecule containing an alkyne group. After washing, the cells are treated with CY5-N3 and a copper catalyst (for CuAAC). The cells are then washed and imaged using a fluorescence microscope or analyzed by flow cytometry.
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| Animal Protocol |
In vivo imaging with CY5-N3-labeled probes is performed using small animal imaging systems. The labeled probe is administered via intravenous injection. At various time points, the animals are anesthetized and imaged using appropriate excitation and emission filters (646/662 nm). The fluorescence signal is quantified to determine the biodistribution and targeting of the probe.
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| ADME/Pharmacokinetics |
CY5-N3 has a molecular weight of 738.92 g/mol and a chemical formula of C36H46N6O7S2. It is highly water-soluble due to its sulfonate groups. This property allows it to be used in purely aqueous buffers, preserving the native conformation and biological activity of labeled biomolecules.
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| Toxicity/Toxicokinetics |
CY5-N3 is generally considered non-toxic for labeling applications. The dye itself has low cytotoxicity, and the concentrations used for labeling are typically low. The safety and toxicity of the final CY5-N3-labeled probe depend on the nature of the biomolecule it is conjugated to.
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| References |
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| Additional Infomation |
CY5-N3 is a valuable tool for bioconjugation and fluorescence imaging. Its azide group allows for specific and efficient labeling via click chemistry. It is used in a variety of applications, including nucleic acid modification, protein localization, and glycobiology research.
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| Molecular Formula |
C36H46N6O7S2
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|---|---|
| Molecular Weight |
738.916446208954
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| Exact Mass |
738.286
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| CAS # |
1621101-43-6
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| PubChem CID |
118986650
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| Appearance |
Brown to reddish brown solid powder
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| LogP |
5.6
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
10
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| Rotatable Bond Count |
15
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| Heavy Atom Count |
51
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| Complexity |
1640
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| Defined Atom Stereocenter Count |
0
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| SMILES |
S(C1C=CC2=C(C=1)C(C)(C)C(/C=C/C=C/C=C1/C(C)(C)C3C=C(C=CC=3N/1CC)S(=O)(=O)[O-])=[N+]2CCCCCC(NCCCN=[N+]=[N-])=O)(=O)(=O)O
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| InChi Key |
LSISYTNZXRYXJU-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C36H46N6O7S2/c1-6-41-30-19-17-26(50(44,45)46)24-28(30)35(2,3)32(41)14-9-7-10-15-33-36(4,5)29-25-27(51(47,48)49)18-20-31(29)42(33)23-12-8-11-16-34(43)38-21-13-22-39-40-37/h7,9-10,14-15,17-20,24-25H,6,8,11-13,16,21-23H2,1-5H3,(H2-,38,43,44,45,46,47,48,49)
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| Chemical Name |
(2E)-2-[(2E,4E)-5-[1-[6-(3-azidopropylamino)-6-oxohexyl]-3,3-dimethyl-5-sulfoindol-1-ium-2-yl]penta-2,4-dienylidene]-1-ethyl-3,3-dimethylindole-5-sulfonate
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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: (1). This product requires protection from light (avoid light exposure) during transportation and storage. (2). This product is not stable in solution, please use freshly prepared working solution for optimal results. |
| 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 : ~25 mg/mL (~33.83 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (3.38 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 (3.38 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. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.3533 mL | 6.7666 mL | 13.5333 mL | |
| 5 mM | 0.2707 mL | 1.3533 mL | 2.7067 mL | |
| 10 mM | 0.1353 mL | 0.6767 mL | 1.3533 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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