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| Targets |
Cyanine5 DBCO does not have a specific biological target as it is a fluorescent labeling reagent. Its function is to provide near-infrared fluorescence for the detection and imaging of azide-labeled biomolecules. The DBCO group reacts specifically with azide groups through a strain-promoted alkyne-azide cycloaddition (SPAAC) click reaction, without the need for copper catalysts. This bioorthogonal conjugation allows for the labeling of proteins, nucleic acids, and other cellular components in living systems.
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| ln Vitro |
Advice (These are our suggested choices; please note that this is merely a guide and should be adjusted to meet your own requirements). Labeling of cells (such as A549 cells) [5][2]: 1. 2. Transfer 2 milliliters of mature seed cells at a density of 3 x 104 (cell-to-cell) into a 35 mm glass-bottomed dish. For three days in a row, add Ac4ManNAz (final concentration of 50 μM) to create azide groups on the cell surface. 3. 4. Use Cyanine5 DBCO (20 μM, final concentration) and wash the cells with DPBS for one hour at 37°C. 5. After rinsing the cells in DPBS (pH 7.4), fix them at 25°C using a mixed formaldehyde-glutaraldehyde fixative. 6. DPBS Stain cells twice (to a pH of 7.4) and mark nuclei with DAPI. 7. Measure the Cyanine5 DBCO fluorophore (Ex=635 nm, Em=650-700 nm) using confocal laser scanning microscopy. Note: 1) Cyanine5 DBCO can inhibit the artificially introduced azide groups on the cell surface for longer than three days when utilizing Ac4ManNAz After treatment. 2) The amount of Cyanine5 DBCO labeling.
Cyanine5 DBCO is used in vitro for fluorescence microscopy, live-cell imaging, and the labeling of azide-functionalized biomolecules. It exhibits excitation at 635 nm and emission at 650-700 nm, providing near-infrared fluorescence. The dye offers high brightness, excellent photostability, and deep tissue penetration. It is used to image azide-labeled biomolecules through a copper-free click reaction. Cyanine5 DBCO can be used for labeling proteins, nucleic acids, and other cellular components. |
| ln Vivo |
Advice (These are our suggested choices; please note that this is merely a guide and can be altered to meet your individual requirements). Tracking cells in vivo[1][2]: 1. Count seeded cells at a density of 3×104 (varies per cell) in a 35 mm glass-bottomed culture dish with 2 mL of growth medium. 2. For three days, add Ac4ManNAz (final concentration of 50 μM) to create azide groups on the cell surface. 3. Use DPBS 4 to wash. After giving the mice anesthesia, inject the cells into the liver's left lobe following treatment with Ac4ManNAz. 5. Put a 200 μL injection of Cyanine5 DBCO (25 μM) into the tail vein that the imaging system identified.
In vivo, Cyanine5 DBCO is used for near-infrared fluorescence imaging of azide-labeled biomolecules. Its near-infrared fluorescence allows for deep tissue penetration and in vivo tracking of proteins, nucleic acids, and other cellular components. The dye's low toxicity makes it suitable for in vivo imaging applications. Cyanine5 DBCO can be used to study molecular interactions and cellular processes in living cells and animal models. |
| Enzyme Assay |
In vitro experiments with Cyanine5 DBCO typically involve preparing stock solutions in DMSO (≥80 mg/mL) and diluting them in assay buffers. For labeling reactions, the compound is incubated with azide-functionalized biomolecules in an appropriate buffer at room temperature for 1-2 hours. The labeled products are then purified by dialysis or chromatography. Fluorescence is measured using a spectrophotometer or imager with excitation at 635 nm and emission at 650-700 nm. The copper-free click reaction ensures compatibility with live-cell labeling.
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| Cell Assay |
In vitro cell-based assays using Cyanine5 DBCO are performed to label and image azide-functionalized biomolecules in live cells. Cells are first incubated with azide-labeled metabolic precursors (e.g., azide-sugars for glycan labeling) to incorporate azide groups into cellular biomolecules. The cells are then treated with Cyanine5 DBCO, which reacts with the azide groups through click chemistry. After washing, cells are imaged by fluorescence microscopy with excitation at 635 nm and emission at 650-700 nm. The dye's near-infrared fluorescence allows for deep tissue imaging with low background.
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| Animal Protocol |
In vivo animal experiments with Cyanine5 DBCO are conducted for near-infrared fluorescence imaging of azide-labeled biomolecules. The dye or Cyanine5 DBCO-labeled molecules are administered intravenously or by other routes to animals. The animals are then imaged using a fluorescence imaging system with excitation at 635 nm and emission at 650-700 nm. The near-infrared fluorescence allows for deep tissue penetration and imaging of molecular interactions and cellular processes in living animals.
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| ADME/Pharmacokinetics |
Dosing and administration of Cyanine5 DBCO for in vivo imaging depend on the specific application. The dye is typically administered intravenously at doses of 1-10 nmol per mouse. Cyanine5 DBCO has a molecular weight of 929.03 g/mol and the formula C53H59F6N4O2P. The compound is stored at -20°C, dry and sealed. It is soluble in DMSO at ≥80 mg/mL. Stock solutions should be stored in aliquots and used within 1 month.
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| Toxicity/Toxicokinetics |
Cyanine5 DBCO is considered to have low toxicity. 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 dye may cause irritation to skin, eyes, and respiratory tract upon contact. The compound's low toxicity makes it suitable for in vivo imaging applications.
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| References |
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| Additional Infomation |
Cyanine5 DBCO (CAS 2360411-64-7) is a near-infrared fluorescent dye conjugate that combines the Cyanine5 fluorophore with a DBCO group. It is also known as DBCO-Cy5 and has the molecular formula C53H59F6N4O2P. The compound is a water-soluble, low-toxicity azide reactive probe for imaging azide-labeled biomolecules by a copper-free click reaction (Ex=635 nm, Em=650-700 nm). Cyanine5 DBCO offers high brightness, excellent photostability, and deep tissue penetration. It is used for fluorescence microscopy, live-cell imaging, and in vivo tracking. The compound is intended for research use only.
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| Molecular Formula |
C53H59F6N4O2P
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| Molecular Weight |
929.05
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| Exact Mass |
928.427
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| CAS # |
2360411-64-7
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| PubChem CID |
164577372
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| Appearance |
Dark purple to black solid powder
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
10
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| Rotatable Bond Count |
15
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| Heavy Atom Count |
66
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| Complexity |
1720
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| Defined Atom Stereocenter Count |
0
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| SMILES |
[P+5]([F-])([F-])([F-])([F-])([F-])[F-].C([N+]1=C(C(C)(C)C2=CC=CC=C12)C=CC=CC=C1N(C2=CC=CC=C2C1(C)C)C)CCCCC(=O)NCCCCCC(N1CC2=CC=CC=C2C#CC2=CC=CC=C12)=O
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| InChi Key |
YPXNDZYXPDFNEL-UHFFFAOYSA-O
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| InChi Code |
InChI=1S/C53H58N4O2.F6P/c1-52(2)43-26-16-19-29-46(43)55(5)48(52)31-9-6-10-32-49-53(3,4)44-27-17-20-30-47(44)56(49)38-22-8-11-33-50(58)54-37-21-7-12-34-51(59)57-39-42-25-14-13-23-40(42)35-36-41-24-15-18-28-45(41)57;1-7(2,3,4,5)6/h6,9-10,13-20,23-32H,7-8,11-12,21-22,33-34,37-39H2,1-5H3;/q;-1/p+1
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| Chemical Name |
N-[6-(2-azatricyclo[10.4.0.04,9]hexadeca-1(16),4,6,8,12,14-hexaen-10-yn-2-yl)-6-oxohexyl]-6-[3,3-dimethyl-2-[5-(1,3,3-trimethylindol-1-ium-2-yl)penta-2,4-dienylidene]indol-1-yl]hexanamide;hexafluorophosphate
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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) |
DMSO : ~125 mg/mL (~134.55 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 | 1.0764 mL | 5.3818 mL | 10.7637 mL | |
| 5 mM | 0.2153 mL | 1.0764 mL | 2.1527 mL | |
| 10 mM | 0.1076 mL | 0.5382 mL | 1.0764 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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