| 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 |
The primary target of Dibenzocyclooctyne-Cy5.5 is not a biological receptor but rather azide-functionalized biomolecules. The DBCO group undergoes rapid and specific reaction with azide groups via strain-promoted alkyne-azide cycloaddition (SPAAC), forming a stable triazole linkage without the need for a copper catalyst, which is often cytotoxic. The Cy5.5 fluorophore serves as a detection label, enabling visualization and tracking of azide-tagged molecules in biological systems.
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| ln Vitro |
In vitro, Dibenzocyclooctyne-Cy5.5 is used to label azide-modified biomolecules such as proteins, peptides, nucleic acids, glycans, and lipids. The DBCO group reacts specifically with azides in a copper-free click reaction at room temperature, typically within 30-120 minutes. This labeling allows for the visualization of cellular components by fluorescence microscopy, flow cytometry, or in-gel fluorescence imaging. The near-infrared fluorescence of Cy5.5 minimizes background autofluorescence and phototoxicity, making it suitable for live-cell imaging.
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| ln Vivo |
Dibenzocyclooctyne-Cy5.5 is not used as a systemic drug and therefore does not have traditional in vivo activity. However, it is used as an imaging probe in live animals for biodistribution studies, tumor imaging, and inflammation detection. When conjugated to an azide-tagged targeting ligand (e.g., antibody, peptide), the Cy5.5 fluorescence allows for non-invasive tracking of the ligand's distribution using NIR fluorescence imaging systems. This enables real-time visualization of disease sites, such as tumors or inflamed tissues, in live mice.
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| Enzyme Assay |
For non-cell-based assay of click conjugation efficiency, a standard protocol uses HPLC or LC-MS analysis. DBCO-Cy5.5 is incubated with an azide-containing molecule (e.g., azido-PEG3-biotin) at a 1:1.2 molar ratio in PBS buffer (pH 7.4) at room temperature for 2 hours. The reaction mixture is then analyzed by reverse-phase HPLC with fluorescence detection (Ex 650 nm, Em 670 nm) and UV-Vis detection. The conversion rate is calculated by comparing the peak areas of the product and residual starting material.
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| Cell Assay |
For in vitro cell labeling experiments, cells are first metabolically labeled with an azide-modified sugar (e.g., Ac4ManNAz for glycan labeling) by culturing in azide-supplemented media for 48-72 hours. Cells are then washed, fixed with 4% paraformaldehyde, and incubated with 5-20 uM DBCO-Cy5.5 in PBS for 30-60 minutes at room temperature. After washing to remove unbound dye, cells are imaged by confocal microscopy or analyzed by flow cytometry to detect Cy5.5 fluorescence.
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| Animal Protocol |
For in vivo imaging studies, a mouse xenograft tumor model is used. Tumor-bearing mice (e.g., with subcutaneous tumors expressing azide-tagged targeting probes) are injected intravenously with DBCO-Cy5.5 (typically 1-5 nmol per mouse) or with a DBCO-Cy5.5 conjugate pre-reacted with an azide-tagged targeting ligand. At various time points (1-72 hours post-injection), mice are anesthetized and imaged using an in vivo NIR fluorescence imaging system with excitation at 640 nm and emission at 700 nm. Fluorescence signal intensity in the tumor region is quantified.
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| ADME/Pharmacokinetics |
As a fluorescent imaging probe, Dibenzocyclooctyne-Cy5.5 is not intended for systemic pharmacokinetic studies as a drug. However, its distribution in vivo can be tracked by NIR fluorescence imaging. The compound has a molecular weight of approximately 1100-1300 Da depending on the PEG spacer length. The DBCO-Cy5.5 conjugate is relatively stable in plasma but may undergo gradual clearance via renal excretion if the molecular weight is below the glomerular filtration cutoff. Tissue distribution can be assessed by ex vivo fluorescence imaging of harvested organs.
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| Toxicity/Toxicokinetics |
Specific toxicity data for Dibenzocyclooctyne-Cy5.5 is not publicly available as it is a research reagent. The compound is not intended for human use. Potential toxicity concerns include the generation of reactive oxygen species from the Cy5.5 fluorophore upon prolonged light exposure (phototoxicity), though this is minimal with near-infrared excitation. The DBCO group is considered bioorthogonal and non-toxic at labeling concentrations. Standard chemical safety precautions (gloves, lab coat, eye protection) should be used when handling the powder.
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| References | |
| Additional Infomation |
Dibenzocyclooctyne-Cy5.5 is a powerful tool for copper-free click chemistry bioorthogonal labeling. The DBCO group is a strained cycloalkyne that reacts with azides rapidly without a copper catalyst, avoiding the cytotoxicity associated with copper-catalyzed reactions. This makes it ideal for live-cell and in vivo labeling applications. The Cy5.5 fluorophore provides deep tissue penetration and low background autofluorescence, enabling non-invasive in vivo imaging. This compound is widely used in chemical biology, glycobiology, and preclinical imaging studies. It is not a pharmaceutical drug.
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| Molecular Formula |
C61H63F6N4O2P
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|---|---|
| Molecular Weight |
1029.14
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| Exact Mass |
1028.459
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| CAS # |
2643308-61-4
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| PubChem CID |
164577381
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| Appearance |
Purple to purplish red 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 |
74
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| Complexity |
1990
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| Defined Atom Stereocenter Count |
0
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| SMILES |
P(F)(F)(F)(F)F.CC1(C(=[N+](CCCCCC(=O)NCCCCCC(N2CC3=CC=CC=C3C#CC3=CC=CC=C23)=O)C2C=CC3=CC=CC=C3C1=2)/C=C/C=C/C=C1\N(C2C=CC3=CC=CC=C3C=2C\1(C)C)C)C.[F-]
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| InChi Key |
CICHRHLVMUNIGJ-UHFFFAOYSA-O
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| InChi Code |
InChI=1S/C61H62N4O2.F6P/c1-60(2)54(63(5)52-39-37-45-24-15-18-28-49(45)58(52)60)31-9-6-10-32-55-61(3,4)59-50-29-19-16-25-46(50)38-40-53(59)64(55)42-22-8-11-33-56(66)62-41-21-7-12-34-57(67)65-43-48-27-14-13-23-44(48)35-36-47-26-17-20-30-51(47)65;1-7(2,3,4,5)6/h6,9-10,13-20,23-32,37-40H,7-8,11-12,21-22,33-34,41-43H2,1-5H3;/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-[1,1-dimethyl-2-[5-(1,1,3-trimethylbenzo[e]indol-3-ium-2-yl)penta-2,4-dienylidene]benzo[e]indol-3-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) |
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 | 0.9717 mL | 4.8584 mL | 9.7169 mL | |
| 5 mM | 0.1943 mL | 0.9717 mL | 1.9434 mL | |
| 10 mM | 0.0972 mL | 0.4858 mL | 0.9717 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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