| Size | Price | Stock | Qty |
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| 1mg |
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| Other Sizes |
| Targets |
JF646 Azide does not target a specific biological receptor. The azide group is a bioorthogonal chemical handle that reacts specifically with alkyne-functionalized molecules via click chemistry. The fluorophore itself is used for visualization. The azide is inert toward biological nucleophiles, enabling specific labeling in complex environments such as live cells or lysates without interfering with native functions.
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| ln Vitro |
Maximum wavelengths for absorption (λabs) and emission (λem) are 646 nm and 664 nm, respectively[1]. For self-labeling tags (like HaloTag), JF646 can function as a ligand[1]. JF646 modifies Azide, according to Janelia Fluor 646.6. With a high extinction coefficient, membrane permeability, and photostability, JF646 is a red fluorescent dye [2].
In cell-free systems, JF646 Azide is used in click chemistry reactions to label alkyne-modified biomolecules. Its photophysical properties (absorption/emission maxima, quantum yield, photostability) are characterized in buffers or organic solvents. The dye exhibits high fluorescence quantum yield (>0.3) and excellent resistance to photobleaching, making it suitable for super-resolution microscopy. The azide group does not affect the dye's spectral properties. |
| ln Vivo |
JF646 Azide itself does not have biological activity; instead, it is used as a labeling reagent. In vitro, it reacts with alkyne-bearing substrates in click chemistry reactions. The labeled products can be visualized by SDS-PAGE, western blot, or fluorescence imaging. The specificity of the azide-alkyne reaction is demonstrated by competitive inhibition with free alkyne or by omitting the copper catalyst (for CuAAC).
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| Enzyme Assay |
A typical cell-free labeling reaction: an alkyne-modified protein (10-50 uM) is incubated with JF646 Azide (20-100 uM) in the presence of CuSO4 (1 mM), THPTA ligand (2 mM), and sodium ascorbate (5 mM) in PBS, pH 7.4, for 1 hour at room temperature. For copper-free SPAAC, a cyclooctyne-modified substrate is used. The reaction is quenched with EDTA, and unbound dye is removed by spin filtration. Labeling efficiency is analyzed by mass spectrometry or fluorescence gel scanning.
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| Cell Assay |
Live or fixed cells expressing alkyne-tagged biomolecules (e.g., via metabolic labeling with alkyne-modified sugars or amino acids) are incubated with JF646 Azide. For copper-free labeling, the azide dye (1-10 uM) is added directly to cell culture medium for 30-60 minutes. For CuAAC, cells must be fixed and permeabilized due to copper toxicity. After washing, cells are imaged by confocal or super-resolution microscopy to visualize the subcellular localization of the tagged biomolecules.
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| Animal Protocol |
For in vivo imaging, JF646 Azide is typically conjugated to a targeting moiety (e.g., alkyne-modified antibody) via click chemistry prior to administration. Alternatively, the free azide dye can be co-injected with a cyclooctyne-modified probe for in vivo click chemistry (pretargeting). In mouse models, the dye-conjugate is administered intravenously (0.5-5 mg/kg). Imaging is performed at 640 nm excitation, and fluorescence signal is monitored over time (0-48 hours). Biodistribution is assessed by organ dissection.
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| ADME/Pharmacokinetics |
JF646 Azide is a small hydrophilic dye with MW ~700-900 Da. Its pharmacokinetics are determined by the conjugate; as a free dye, it is rapidly cleared by renal excretion. The azide group is chemically stable in blood for several hours. The dye shows minimal non-specific protein binding. It should be stored at -20degC protected from light. The click reaction kinetics are fast, with half-lives of minutes to hours depending on the alkyne partner.
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| Toxicity/Toxicokinetics |
JF646 Azide exhibits low toxicity at working concentrations (≤10 uM in cells). Copper-catalyzed click reactions require Cu(I), which can be cytotoxic; therefore, copper-free protocols are preferred for live cells. No acute or chronic toxicity has been reported for the dye alone. Standard laboratory safety practices should be followed. The compound is not for clinical use; formal toxicology studies are not available.
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| References |
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| Additional Infomation |
JF646 Azide is a research-grade fluorescent probe developed by Janelia Research Campus. It is part of the Janelia Fluor® series optimized for single-molecule localization microscopy (SMLM) and STED. The azide derivative enables bioorthogonal labeling of alkyne-tagged molecules in live cells, tissues, and organisms. It is not approved for diagnostic or therapeutic applications. The dye is compatible with various imaging platforms.
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| Molecular Formula |
C37H44N6O6SI
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|---|---|
| Molecular Weight |
696.87
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| Related CAS # |
Janelia Fluor® 646, SE;1811539-59-9;Janelia Fluor® 646 TFA;Janelia Fluor® 646, Maleimide
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| Appearance |
Light green to green solid powder
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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). Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture. |
| 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) |
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.4350 mL | 7.1749 mL | 14.3499 mL | |
| 5 mM | 0.2870 mL | 1.4350 mL | 2.8700 mL | |
| 10 mM | 0.1435 mL | 0.7175 mL | 1.4350 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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