| Size | Price | Stock | Qty |
|---|---|---|---|
| 1mg |
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| Other Sizes |
| Targets |
SiR-DBCO is a fluorescent labeling reagent that does not have a specific pharmacological target. The DBCO group enables bioorthogonal click chemistry with azide-containing molecules. This allows for specific labeling of azide-modified biomolecules in live cells or biological samples without the need for copper catalysts, which can be toxic to living systems.
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|---|---|
| ln Vitro |
As a fluorescent probe, SiR-DBCO itself does not possess pharmacological activity. Its utility lies in its photophysical properties: the silicon-rhodamine fluorophore provides far-red to near-infrared fluorescence with excellent brightness, photostability, and cell permeability. The DBCO functionality enables efficient SPAAC conjugation to azide-modified targets.
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| ln Vivo |
As a fluorescent probe, SiR-DBCO is used for in vivo imaging applications. When conjugated to azide-modified targeting moieties via SPAAC, the dye enables visualization of specific biomarkers in living organisms. The far-red to near-infrared fluorescence allows for deep tissue penetration and reduced autofluorescence, making it suitable for preclinical imaging studies.
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| Enzyme Assay |
Non-cell-based protocols for SiR-DBCO involve click chemistry conjugation and dye characterization. A typical conjugation procedure includes: dissolving SiR-DBCO in anhydrous DMSO, adding to a solution of azide-modified target molecule in appropriate buffer (PBS, pH 7.4), incubating at room temperature for 1–4 hours, and purifying the conjugate by size-exclusion chromatography or HPLC. Conjugation efficiency is confirmed by mass spectrometry or SDS-PAGE with fluorescence detection.
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| Cell Assay |
Cellular assays with SiR-DBCO typically involve labeling azide-modified biomolecules in live cells. A representative protocol includes: culturing cells with azide-modified metabolic precursors (e.g., Ac₄ManNAz for glycan labeling, or AHA for protein labeling), washing, incubating with SiR-DBCO (0.1–5 μM) for 30–60 minutes at 37°C, washing to remove unbound dye, and imaging using confocal microscopy with far-red excitation/emission settings. The dye's cell permeability allows for live-cell imaging without fixation.
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| Animal Protocol |
In vivo animal imaging studies with SiR-DBCO typically involve administration of the dye-conjugate via intravenous injection. A representative protocol includes: injecting SiR-DBCO-labeled probe into mouse models, allowing circulation and distribution for 1–24 hours, performing whole-body fluorescence imaging using an in vivo imaging system with appropriate far-red excitation/emission filters, and harvesting tissues for ex vivo biodistribution analysis.
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| ADME/Pharmacokinetics |
Pharmacokinetic properties are determined for the SiR-DBCO conjugate rather than the dye itself. Typical PK parameters for SiR-based probes include rapid clearance from circulation, distribution depending on the targeting moiety, and excretion primarily via renal or hepatobiliary routes. The far-red fluorescence allows for real-time monitoring of biodistribution.
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| Toxicity/Toxicokinetics |
As a fluorescent dye for research use, SiR-DBCO is not intended for human therapeutic use. Standard safety precautions should be followed when handling the dye. The compound should be stored at -20°C, protected from light. The DBCO group is reactive with azides and should be handled with appropriate care to avoid unintended reactions.
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| References | |
| Additional Infomation |
SiR-DBCO (CAS 2259859-41-9) is a versatile tool for bioorthogonal labeling and live-cell imaging. The combination of the silicon-rhodamine fluorophore (excellent brightness, photostability, and cell permeability) and DBCO click chemistry (copper-free, bioorthogonal) enables specific labeling of azide-modified biomolecules in complex biological environments. This reagent is widely used in chemical biology and molecular imaging for studying dynamic biological processes in living cells and organisms.
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| Molecular Formula |
C45H42N4O4SI
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|---|---|
| Molecular Weight |
730.92
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| Exact Mass |
730.297
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| CAS # |
2259859-41-9
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| PubChem CID |
162405156
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| Appearance |
Blue to blue-green solid powder
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| Hydrogen Bond Donor Count |
1
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| Hydrogen Bond Acceptor Count |
6
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| Rotatable Bond Count |
6
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| Heavy Atom Count |
54
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| Complexity |
1460
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CN(C)C1=CC2=C(C=C1)C3(C4=C([Si]2(C)C)C=C(C=C4)N(C)C)C5=C(C=CC(=C5)C(=O)NCCC(=O)N6CC7=CC=CC=C7C#CC8=CC=CC=C86)C(=O)O3
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| InChi Key |
XAKLGZMKEDUDBM-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C45H42N4O4Si/c1-47(2)33-18-21-36-40(26-33)54(5,6)41-27-34(48(3)4)19-22-37(41)45(36)38-25-31(17-20-35(38)44(52)53-45)43(51)46-24-23-42(50)49-28-32-13-8-7-11-29(32)15-16-30-12-9-10-14-39(30)49/h7-14,17-22,25-27H,23-24,28H2,1-6H3,(H,46,51)
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| Chemical Name |
N-[3-(2-azatricyclo[10.4.0.04,9]hexadeca-1(16),4,6,8,12,14-hexaen-10-yn-2-yl)-3-oxopropyl]-3',7'-bis(dimethylamino)-5',5'-dimethyl-1-oxospiro[2-benzofuran-3,10'-benzo[b][1]benzosiline]-5-carboxamide
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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) |
Typically soluble in DMSO (e.g. 10 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 | 1.3681 mL | 6.8407 mL | 13.6814 mL | |
| 5 mM | 0.2736 mL | 1.3681 mL | 2.7363 mL | |
| 10 mM | 0.1368 mL | 0.6841 mL | 1.3681 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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