| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| 10mg |
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| Other Sizes |
| Targets |
JF646 TFA does not target a specific receptor or enzyme. The free acid form contains a carboxylate group that can be activated (e.g., to NHS ester) for covalent labeling. The fluorophore itself is used for non-covalent staining of hydrophobic environments or as a tracer. The TFA salt improves solubility and facilitates handling. No specific biological target is engaged; the dye is an optical tool.
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| ln Vitro |
JF646 TFA: λmax(nm)=646, λem(nm) =664[1].
In cell-free assays, JF646 TFA is characterized by its absorption and emission spectra in various solvents. The free acid form has a high extinction coefficient (typically >100,000 M-¹cm-¹) and good quantum yield (~0.3-0.5). Photostability is measured by continuous illumination; JF646 TFA resists bleaching for extended periods, making it suitable for time-lapse and super-resolution microscopy. The TFA counterion does not affect spectral properties. |
| ln Vivo |
JF646 TFA is not used in typical bioactivity assays. However, its spectral properties allow it to serve as a fluorescence standard for instrument calibration, for quantifying labeling efficiency, or as a non-reactive control in cellular uptake studies. It can also be used for direct (non-covalent) staining of lipophilic compartments due to its moderate hydrophobicity, though specific labeling is not guaranteed.
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| Enzyme Assay |
The purity and identity of JF646 TFA are confirmed by HPLC and mass spectrometry. For use as a standard, the compound is dissolved in DMSO to prepare a stock solution (1-10 mM). UV-Vis absorption is measured to determine concentration (using the extinction coefficient at λmax). Fluorescence emission is recorded using a spectrofluorometer. The compound is stable in DMSO at -20degC for months. For cell-free binding studies, it can be used as a control for non-specific fluorescence.
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| Cell Assay |
Cells are incubated with JF646 TFA (0.1-10 uM) in culture medium for 15-60 minutes, then washed. The dye may accumulate in lysosomes or lipid droplets due to its physicochemical properties. Cellular fluorescence is imaged by confocal microscopy. As a control, cells can be pre-treated with the reactive form (e.g., JF646 NHS) to compare specific versus non-specific staining. No target-specific signal is expected; any observed fluorescence indicates non-specific uptake.
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| Animal Protocol |
JF646 TFA can be administered intravenously to mice (e.g., 0.5-2 mg/kg) as a tracer for imaging or to assess dye biodistribution. Fluorescence is imaged using near-infrared systems. The free dye is rapidly cleared from circulation via renal filtration, with a half-life of minutes. Accumulation in the liver and spleen may occur if the dye aggregates. Ex vivo organ imaging at 1-24 hours post-injection shows signal primarily in the kidneys and bladder, confirming renal clearance.
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| ADME/Pharmacokinetics |
JF646 TFA has a molecular weight around 700 Da. It is highly soluble in DMSO and moderately soluble in aqueous buffers (with TFA salt). The free acid form has limited cell permeability due to the negative charge. In vivo, it shows rapid distribution and elimination. The plasma half-life in mice is approximately 10-30 minutes. The dye is not metabolized significantly; it is excreted unchanged. The compound should be stored at -20degC away from light.
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| Toxicity/Toxicokinetics |
JF646 TFA is used only in small amounts for research; no significant toxicity has been reported. At concentrations up to 10 uM in cell culture, no adverse effects on viability or morphology are observed. In mice, doses up to 10 mg/kg have been administered without visible toxicity. The TFA counterion is present at low, non-toxic levels. Standard safety precautions (gloves, lab coat) are sufficient. No clinical toxicity data exist.
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| References | |
| Additional Infomation |
JF646 TFA is a research-use-only fluorescent dye from the Janelia Fluor® family. It is not approved for clinical or diagnostic use. The free acid form is a precursor for synthesizing reactive derivatives (NHS ester, maleimide, azide). It can also serve as a non-covalent stain for certain applications. The dye is optimized for high brightness and photostability, enabling advanced microscopy techniques such as STED, PALM, and confocal imaging. Store protected from light.
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| Molecular Formula |
C31H29F3N2O6SI
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| Molecular Weight |
610.65
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| Related CAS # |
Janelia Fluor® 646, SE;1811539-59-9;Janelia Fluor® 646, Azide;Janelia Fluor® 646, Maleimide
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| Appearance |
Blue to dark blue 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: Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture and light. |
| 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 (~163.76 mM)
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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 | 1.6376 mL | 8.1880 mL | 16.3760 mL | |
| 5 mM | 0.3275 mL | 1.6376 mL | 3.2752 mL | |
| 10 mM | 0.1638 mL | 0.8188 mL | 1.6376 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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