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JOE phosphoramidite, 6-isomer
| Catalog Number | A19-0092 |
| Category | DNA Stains |
| Molecular Formula | C48H60N3Cl2O12P |
| Molecular Weight | 972.88 |
| Catalog Number | Size | Price | Quantity |
|---|---|---|---|
| A19-0092 | -- | $-- |
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Product Introduction
JOE phosphoramidite for oligonucleotide synthesis, pure 6-isomer (6-JOE).,Fluorescent dye JOE is a fluorescein derivative containing two chlorine atoms and two methoxy groups. Its absorption and emission maxima are at 503 nm and 525 nm, respectively. By its spectral characteristics JOE is found in between FAM and TAMRA/ROX; therefore, this fluorophor is commonly used for multiplex detection, including that during DNA sequencing.,Our catalog also contains
JOE phosphoramidite, 5-isomer.
We
compared qPCR probes containing different JOE isomers (5-JOE and 6-JOE) and did not find any
significant differences between them.,Coupling: 6 minutes,Deprotection: standard conditions using ammonium hydroxide; deprotection time depends on oligonucleotide composition and nucleobase protecting groups (deprotection for 17 h at 55 °С removes all protecting groups from standard nucleobases). AMA (solution of 30% ammonium hydroxide/40% aqueous methylamine 1:1 v/v) can be used with ~5% of non-fluorescent side product forming. To avoid formation of the side product, start deprotection with ammonium hydroxide (30 min at room temperature), then add an equal volume of 40% aqueous methylamine and continue deprotection as required with AMA (e.g. 10 min at 65 °C).
Chemical Information |
|
|---|---|
| Purity | NMR 1H and 31P, HPLC-MS |
| IUPAC Name | [4',5'-dichloro-6-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexylcarbamoyl]-6'-(2,2-dimethylpropanoyloxy)-2',7'-dimethoxy-3-oxospiro[2-benzofuran-1,9'-xanthene]-3'-yl] 2,2-dimethylpropanoate |
| Canonical SMILES | CC(C)N(C(C)C)P(OCCCCCCNC(=O)C1=CC2=C(C=C1)C(=O)OC23C4=CC(=C(C(=C4OC5=C(C(=C(C=C35)OC)OC(=O)C(C)(C)C)Cl)Cl)OC(=O)C(C)(C)C)OC)OCCC#N |
| InChI | InChI=1S/C48H60Cl2N3O12P/c1-27(2)53(28(3)4)66(61-23-17-20-51)60-22-16-14-13-15-21-52-42(54)29-18-19-30-31(24-29)48(65-43(30)55)32-25-34(58-11)40(63-44(56)46(5,6)7)36(49)38(32)62-39-33(48)26-35(59-12)41(37(39)50)64-45(57)47(8,9)10/h18-19,24-28H,13-17,21-23H2,1-12H3,(H,52,54) |
| InChI Key | CKBMUCQWGUZAKQ-UHFFFAOYSA-N |
| Solubility | Good solubility in acetonitrile and DCM |
| Appearance | White solid |
- Product Specification
- Application
| CF260 | 0.36 |
| CF280 | 0.28 |
| Excitation | 533 |
| Emission | 554 |
| Storage | Storage: 12 months after receival at -20 °C in the Dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate. |
JOE phosphoramidite, 6-isomer, a fluorescent labeling reagent utilized in molecular biology and biochemistry, finds diverse applications. Here are four key applications of JOE phosphoramidite, 6-isomer:
DNA Sequencing: A cornerstone in molecular research, JOE phosphoramidite is instrumental in synthesizing fluorescently labeled oligonucleotides for DNA sequencing. By integrating JOE-labeled nucleotides into DNA strands, researchers can achieve precise and high-throughput detection of sequence data on fluorescence-based platforms. This meticulous approach elevates the accuracy and efficiency of sequencing technologies, propelling advancements in genetic analysis.
Real-Time PCR: In the dynamic realm of real-time PCR assays, JOE phosphoramidite plays a vital role in labeling probes for detecting and quantifying specific DNA sequences. The fluorescence emitted by JOE-labeled probes facilitates real-time monitoring of amplification processes, crucial for applications like gene expression profiling and pathogen identification. This real-time fluorescence tracking enhances the speed and accuracy of DNA analysis, shaping the future of molecular diagnostics.
Molecular Probes: Harnessing the power of JOE phosphoramidite, researchers can craft molecular probes for a myriad of hybridization assays. These fluorescent probes selectively bind to complementary DNA or RNA sequences, enabling visualization and quantification. This versatile application finds utility in diagnostics, in situ hybridization techniques, and diverse research endeavors, amplifying possibilities in molecular exploration.
Genotyping: By incorporating JOE-labeled oligonucleotides, researchers unlock the potential to distinguish between alleles in genotyping assays. The distinct fluorescent signals emitted by JOE markers are captured and analyzed to decipher genetic variations, driving progress in genetic research, personalized medicine, and agricultural breeding programs. This innovative approach revolutionizes genetic analysis, opening new avenues for tailored medical treatments and crop enhancement strategies.
Computed Properties | |
|---|---|
| XLogP3 | 9.7 |
| Hydrogen Bond Donor Count | 1 |
| Hydrogen Bond Acceptor Count | 14 |
| Rotatable Bond Count | 23 |
| Exact Mass | 971.3291667 g/mol |
| Monoisotopic Mass | 971.3291667 g/mol |
| Topological Polar Surface Area | 181Ų |
| Heavy Atom Count | 66 |
| Formal Charge | 0 |
| Complexity | 1650 |
| Isotope Atom Count | 0 |
| Defined Atom Stereocenter Count | 0 |
| Undefined Atom Stereocenter Count | 1 |
| Defined Bond Stereocenter Count | 0 |
| Undefined Bond Stereocenter Count | 0 |
| Covalently-Bonded Unit Count | 1 |
| Compound Is Canonicalized | Yes |
Applications of Fluorescent Probes & Dyes
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