| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| 10mg |
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| Targets |
Cyanine5 azide chloride is not a pharmaceutical drug and does not target a biological receptor. Instead, it functions as a chemical labeling tool where the azide group serves as a bioorthogonal handle for click chemistry conjugation. The azide group specifically reacts with alkyne-functionalized molecules (terminal alkynes via CuAAC or strained alkynes like DBCO via SPAAC) to form stable triazole linkages. This enables fluorescent tagging of alkyne-modified biomolecules for detection and imaging purposes.
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| ln Vitro |
In vitro, Cyanine5 azide chloride is used for the fluorescence labeling of alkyne-modified biomolecules such as proteins, peptides, nucleic acids, and glycans. The azide group undergoes copper-catalyzed azide-alkyne cycloaddition (CuAAC) with terminal alkynes, forming a stable triazole linkage. It also participates in strain-promoted azide-alkyne cycloaddition (SPAAC) with molecules containing DBCO (dibenzocyclooctyne) or BCN (bicyclononyne) groups, eliminating the need for a cytotoxic copper catalyst. The strong fluorescence (λex=646 nm, λem=662 nm) enables detection by fluorescence microscopy, flow cytometry, or in-gel fluorescence imaging.
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| ln Vivo |
In vivo, Cyanine5 azide chloride is not administered directly but can be used to pre-label alkyne-functionalized biomolecules for in vivo imaging applications. The near-infrared fluorescence (ex/em 646/662 nm) allows for deep tissue penetration with minimal background autofluorescence, making it suitable for tracking the biodistribution of alkyne-modified drugs, antibodies, or nanoparticles in live animals. The azide functionality enables bioorthogonal labeling without interfering with the biological activity of the target molecule. Cyanine5 azide can be detected in small quantities (nM) by the naked human eye.
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| Enzyme Assay |
For non-cell-based click conjugation assays, a standard protocol involves the copper-catalyzed click reaction between Cyanine5 azide chloride and an alkyne-containing molecule. Alkyne-functionalized biomolecule (0.5-1 mg/mL) is mixed with Cyanine5 azide chloride (10-20 uM) in PBS buffer (pH 7.4) containing 1 mM CuSO4 and 2 mM sodium ascorbate as reducing agent. The reaction is incubated at room temperature for 2 hours. For strain-promoted click chemistry, Cyanine5 azide chloride is mixed with DBCO-functionalized molecule (1:1 molar ratio) in PBS buffer at room temperature for 30-60 minutes without copper. The conjugation efficiency is analyzed by SDS-PAGE followed by fluorescence scanning or by HPLC.
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| Cell Assay |
For in vitro cell-based assays, cells are first metabolically labeled with an alkyne-modified sugar (e.g., Ac4ManNAk for glycan labeling) or alkyne-functionalized amino acids for 24-48 hours. Alternatively, alkyne-labeled antibodies or targeting ligands are used. Cells are then fixed with 4% paraformaldehyde, permeabilized with 0.1% Triton X-100 if necessary, and incubated with 5-20 uM Cyanine5 azide chloride in PBS for 30-60 minutes at room temperature. Click chemistry additives (CuSO4, sodium ascorbate, and THPTA ligand) are added for CuAAC reactions. For SPAAC, no copper is needed. After washing, cells are imaged by confocal microscopy (Ex/Em 640 nm/660 nm) or analyzed by flow cytometry.
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| Animal Protocol |
For in vivo animal studies, a mouse xenograft tumor model can be used. A tumor-targeting antibody or peptide is first functionalized with an alkyne or DBCO group. This conjugate is then clicked ex vivo with Cyanine5 azide chloride using the SPAAC reaction (no copper) in PBS for 1-2 hours at room temperature. The labeled conjugate (100-200 ug in 200 uL PBS) is purified and administered intravenously to nude mice bearing subcutaneous tumor xenografts. Mice are imaged at 1, 6, 24, 48, and 72 hours post-injection using an in vivo imaging system with 640 nm excitation and 670 nm emission filters. Organ distribution is assessed by ex vivo imaging of harvested organs.
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| ADME/Pharmacokinetics |
Cyanine5 azide chloride has a molecular weight of 601.22 g/mol and absorption/emission maxima of 646 nm/662 nm in PBS buffer. The extinction coefficient is 250,000 L·mol-¹·cm-¹, and the quantum yield (Φ) is 0.2. The compound is soluble in DMSO, DMF, and DCM, with DMSO solubility of ~100 mg/mL. The product appears as a light brown to brown solid powder and should be stored at -20degC protected from light. In solution, it is stable for 6 months at -80degC or 1 month at -20degC. The compound is prepared as a 10 mM stock solution in DMSO for labeling experiments.
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| Toxicity/Toxicokinetics |
The azide group may be reduced by dithiothreitol (DTT) or other reducing agents, so these should be avoided in labeling buffers. Standard chemical safety precautions (gloves, lab coat, safety goggles) should be used when handling this compound. Avoid inhalation of dust and contact with skin and eyes. In solution, the dye should be protected from light to prevent photobleaching. This compound is not intended for human therapeutic or diagnostic use and should be treated as a research chemical. No specific acute toxicity data is available.
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| References | |
| Additional Infomation |
Cyanine5 azide chloride is a water-soluble fluorescent dye that contains an azide group for click chemistry reactions. The Cy5 fluorophore is suitable for many fluorescence detection methods and can be easily detected in small quantities (nM) by the naked human eye. The compound can undergo both copper-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) with molecules containing DBCO or BCN groups. Cyanine5 azide chloride is widely used in chemical biology for labeling alkyne-modified biomolecules and for glycan imaging. This product is for research use only and is not for clinical diagnostics or therapy.
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| Molecular Formula |
C35H45CLN6O
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| Molecular Weight |
601.224406957626
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| Exact Mass |
600.334
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| CAS # |
1267539-32-1
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| Related CAS # |
1267539-32-1 (chloride);1267804-34-1 (cation);
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| PubChem CID |
131954329
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| Appearance |
Light brown to brown solid powder
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
5
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| Rotatable Bond Count |
13
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| Heavy Atom Count |
43
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| Complexity |
1110
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CC1(C2=CC=CC=C2[N+](=C1/C=C/C=C/C=C/3\C(C4=CC=CC=C4N3CCCCCC(=O)NCCCN=[N+]=[N-])(C)C)C)C.[Cl-]
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| InChi Key |
QENDFXAAWUTRRV-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C35H44N6O.ClH/c1-34(2)27-17-11-13-19-29(27)40(5)31(34)21-8-6-9-22-32-35(3,4)28-18-12-14-20-30(28)41(32)26-15-7-10-23-33(42)37-24-16-25-38-39-36;/h6,8-9,11-14,17-22H,7,10,15-16,23-26H2,1-5H3;1H
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| Chemical Name |
N-(3-azidopropyl)-6-[(2E)-3,3-dimethyl-2-[(2E,4E)-5-(1,3,3-trimethylindol-1-ium-2-yl)penta-2,4-dienylidene]indol-1-yl]hexanamide;chloride
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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 (~166.33 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 | 1.6633 mL | 8.3164 mL | 16.6328 mL | |
| 5 mM | 0.3327 mL | 1.6633 mL | 3.3266 mL | |
| 10 mM | 0.1663 mL | 0.8316 mL | 1.6633 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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