
6-JOE Alkyne
| Catalog Number | R02-0028 |
| Category | Alkynes |
| Molecular Formula | C26H17Cl2NO8 |
| Molecular Weight | 542.32 |
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Product Introduction
6-JOE Alkyne is a fluorescent labeling reagent featuring a 6-carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein (6-JOE) fluorophore conjugated to an alkyne functional group. The alkyne moiety enables bioorthogonal click chemistry reactions, particularly copper-catalyzed or strain-promoted azide-alkyne cycloaddition, allowing selective and efficient labeling of biomolecules. It is used in oligonucleotide modification, surface functionalization, and bioconjugation applications.
Chemical Information
Product Specification
Application
Computed Properties
Chemical Information
| Synonyms | JOE alkyne, 6-isomer; 4',5'-Dichloro-3',6'-dihydroxy-2',7'-dimethoxy-3-oxo-N-(prop-2-yn-1-yl)-3H-spiro[isobenzofuran-1,9'-xanthene]-6-carboxamide; Spiro[isobenzofuran-1(3H),9'-[9H]xanthene]-6-carboxamide, 4',5'-dichloro-3',6'-dihydroxy-2',7'-dimethoxy-3-oxo-N-2-propyn-1-yl-; 4',5'-Dichloro-3',6'-dihydroxy-2',7'-dimethoxy-3-oxo-N-(2-propyn-1-yl)-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxamide |
| Purity | NMR 1H, HPLC-MS (95%) |
| IUPAC Name | 4',5'-dichloro-3',6'-dihydroxy-2',7'-dimethoxy-1-oxo-N-prop-2-ynylspiro[2-benzofuran-3,9'-xanthene]-5-carboxamide |
| SMILES | COC1=C(C(=C2C(=C1)C3(C4=CC(=C(C(=C4O2)Cl)O)OC)C5=C(C=CC(=C5)C(=O)NCC#C)C(=O)O3)Cl)O |
| InChI | InChI=1S/C26H17Cl2NO8/c1-4-7-29-24(32)11-5-6-12-13(8-11)26(37-25(12)33)14-9-16(34-2)20(30)18(27)22(14)36-23-15(26)10-17(35-3)21(31)19(23)28/h1,5-6,8-10,30-31H,7H2,2-3H3,(H,29,32) |
| InChIKey | FITDEERKHNKYNG-UHFFFAOYSA-N |
| Solubility | Soluble in DMF, DMSO |
| Appearance | Orange solid |
Product Specification
| ε, L⋅mol-1⋅cm-1 | 75000 |
| Excitation | 533 |
| Emission | 554 |
| Storage | Store at -20 °C |
Application
JOE alkyne 6-isomer, a versatile fluorescent dye, finds extensive application in molecular and cellular biology. Here are four key applications:
Fluorescent Labeling: JOE alkyne 6-isomer serves as a pivotal tool for labeling biomolecules such as nucleic acids and proteins through click chemistry reactions. This specialized fluorescent labeling technique enables researchers to visualize and track specific molecules within intricate biological systems. By leveraging this method, scientists delve into cellular processes like DNA replication, transcription, and protein-protein interactions in real-time, unraveling the dynamic intricacies of biomolecular interactions.
Flow Cytometry: In the realm of flow cytometry, JOE alkyne 6-isomer plays a critical role in staining cells for sorting and analysis. Through conjugation of this dye to antibodies or other targeting molecules, distinct cell populations can be discerned and quantified based on their unique fluorescence signals. This application is integral for immunophenotyping, cell cycle analysis, and exploring cellular responses to diverse treatments, shedding light on the cellular landscape with precision and clarity.
Fluorescence Microscopy: Renowned for its exceptional performance in fluorescence microscopy, JOE alkyne 6-isomer enables high-resolution imaging of cellular structures and dynamics. Its vibrant fluorescence and robust stability render it ideal for both live-cell imaging and fixed samples, offering insights into intricate cellular architecture, intracellular trafficking, and the spatial arrangement of biomolecules.
Quantitative PCR (qPCR): A key player in quantitative PCR assays, JOE alkyne 6-isomer acts as a fluorescent reporter molecule, facilitating the precise quantification of nucleic acids. By monitoring the fluorescence signal during the amplification process, researchers can delve into gene expression analysis, pathogen detection, and genetic variation studies with unparalleled accuracy.
Computed Properties
| XLogP3 | 4 |
| Hydrogen Bond Donor Count | 3 |
| Hydrogen Bond Acceptor Count | 8 |
| Rotatable Bond Count | 4 |
| Exact Mass | 541.0331219 g/mol |
| Monoisotopic Mass | 541.0331219 g/mol |
| Topological Polar Surface Area | 124Ų |
| Heavy Atom Count | 37 |
| Formal Charge | 0 |
| Complexity | 920 |
| Isotope Atom Count | 0 |
| Defined Atom Stereocenter Count | 0 |
| Undefined Atom Stereocenter Count | 0 |
| Defined Bond Stereocenter Count | 0 |
| Undefined Bond Stereocenter Count | 0 |
| Covalently-Bonded Unit Count | 1 |
| Compound Is Canonicalized | Yes |
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