for sensitive chromatographic and analytical workflows requiring minimal baseline interference.
Room temperature Ships Check lot-specific COA for exact specifications.
SDS, COA, datasheet, and spec sheet available for download. Lot-specific COA accessible via lot number lookup.
Cited in 1 peer-reviewed publications across chromatography, organic synthesis, and cross-coupling reactions.
Ex(nm):494
Em(nm):522
Solvent：MeCN
Features and Biological Applications
There are several ways of labeling an oligonucleotide with fluorescein. The choice of label is diversified further, depending on the spectral requirements. 5’-fluorescein-CE phosphoramidite, derived from the single isomer 6-carboxyfluorescein, 5’-hexachlorofluorescein-CE phosphoramidite (HEX) and 5’-tetrachlorofluorescein-CE phosphoramidite (TET) can all be used to efficiently label an oligonucleotide at the 5’-end. Labeling the 3’-end of an oligo with fluorescein can be achieved using 3’-Fluorescein CPGs. Standard cleavage and deprotection with ammonium hydroxide liberates the fluorescein-labeled oligo when using any of these supports.
References
1. Browne KA. (2005) Sequence-specific, self-reporting hairpin inversion probes. J Am Chem Soc, 127, 1989.
2.Dobson N, McDowell DG, French DJ, Brown LJ, Mellor JM, Brown T. (2003) Synthesis of HyBeacons and dual-labelled probes containing 2'-fluorescent groups for use in genetic analysis. Chem Commun (Camb), 1234.
3. Hagmar P, Bailey M, Tong G, Haralambidis J, Sawyer WH, Davidson BE. (1995) Synthesis and characterisation of fluorescent oligonucleotides. Effect of internal labelling on protein recognition. Biochim Biophys Acta, 1244, 259.
4. Hakala H, Virta P, Salo H, Lonnberg H. (1998) Simultaneous detection of several oligonucleotides by time-resolved fluorometry: the use of a mixture of categorized microparticles in a sandwich type mixed-phase hybridization assay. Nucleic Acids Res, 26, 5581.
5. Hill KW, Taunton-Rigby J, Carter JD, Kropp E, Vagle K, Pieken W, McGee DP, Husar GM, Leuck M, Anziano DJ, Sebesta DP. (2001) Diels--Alder bioconjugation of diene-modified oligonucleotides. J Org Chem, 66, 5352.
6. Kim SJ, Bang EK, Kwon HJ, Shim JS, Kim BH. (2004) Modified oligonucleotides containing lithocholic acid in their backbones: their enhanced cellular uptake and their mimicking of hairpin structures. Chembiochem, 5, 1517.
7. Kutyavin IV, Lokhov SG, Afonina IA, Dempcy R, Gall AA, Gorn VV, Lukhtanov E, Metcalf M, Mills A, Reed MW, Sanders S, Shishkina I, Vermeulen NM. (2002) Reduced aggregation and improved specificity of G-rich oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine bases. Nucleic Acids Res, 30, 4952.
8. Lee SP, Censullo ML, Kim HG, Knutson JR, Han MK. (1995) Characterization of endonucleolytic activity of HIV-1 integrase using a fluorogenic substrate. Anal Biochem, 227, 295.
9. Meyer KL, Hanna MM. (1996) Synthesis and characterization of a new 5-thiol-protected deoxyuridine phosphoramidite for site-specific modification of DNA. Bioconjug Chem, 7, 401.
| Sonrisas canónicas | CC(C)N(C(C)C)P(OCCCCCCNC(=O)C1=CC2=C(C=C1)C(=O)OC23C4=C(C=C(C=C4)OC(=O)C(C)(C)C)OC5=C3C=CC(=C5)OC(=O)C(C)(C)C)OCCC#N |
|---|---|
| IUPAC Name | [6-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexylcarbamoyl]-6'-(2,2-dimethylpropanoyloxy)-3-oxospiro[2-benzofuran-1,9'-xanthene]-3'-yl] 2,2-dimethylpropanoate |
| InChIKey | MGPYJVWEJNTXLC-UHFFFAOYSA-N |
| INCHI | 1S/C46H58N3O10P/c1-29(2)49(30(3)4)60(55-25-15-22-47)54-24-14-12-11-13-23-48-40(50)31-16-19-34-37(26-31)46(59-41(34)51)35-20-17-32(56-42(52)44(5,6)7)27-38(35)58-39-28-33(18-21-36(39)46)57-43(53)45(8,9)10/h16-21,26-30H,11-15,23-25H2,1-10H3,(H,48,50) |
| Isómeros SMILES | CC(C)N(C(C)C)P(OCCCCCCNC(=O)C1=CC2=C(C=C1)C(=O)OC23C4=C(C=C(C=C4)OC(=O)C(C)(C)C)OC5=C3C=CC(=C5)OC(=O)C(C)(C)C)OCCC#N |
| Peso molecular | 843.94 |
| Reaxy-Rn | 9749790 |
| Reaxys-RN_link_address | https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=9749790&ln= |
Comprehensive hazard, handling, storage, and regulatory compliance document.
Download SDS →Lot-specific quality data. Enter your lot number to retrieve the exact COA.
Look up COA →Full quality attributes and acceptance criteria for this grade.
View spec sheet →Taxonomy Tree
| Kingdom | Organic compounds |
|---|---|
| Superclass | Organoheterocyclic compounds |
| Clase | Benzopyrans |
| Subclass | 1-benzopyrans |
| Intermediate Tree Nodes | Dibenzopyrans |
| Direct Parent | Xanthenes |
| Alternative Parents | Diarylethers Phthalides Phenol esters Benzofuranones Isobenzofurans Dicarboxylic acids and derivatives Secondary carboxylic acid amides Lactones Carboxylic acid esters Oxacyclic compounds Nitriles Organic oxides Hydrocarbon derivatives Carbonyl compounds |
| Molecular Framework | Aromatic heteropolycyclic compounds |
| Substituents | Xanthene - Diaryl ether - Benzofuranone - Phenol ester - Phthalide - Isobenzofuranone - Isocoumaran - Isobenzofuran - Benzenoid - Dicarboxylic acid or derivatives - Carboxamide group - Carboxylic acid ester - Secondary carboxylic acid amide - Lactone - Oxacycle - Carboxylic acid derivative - Ether - Carbonitrile - Nitrile - Carbonyl group - Organic oxide - Organic oxygen compound - Cyanide - Organic nitrogen compound - Hydrocarbon derivative - Organonitrogen compound - Organooxygen compound - Aromatic heteropolycyclic compound |
| Descripción | This compound belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring. |
| External Descriptors | Not available |
| Peso molecular | 843.900 g/mol |
|---|---|
| XLogP3 | 8.500 |
| Hydrogen Bond Donor Count | 1 |
| Hydrogen Bond Acceptor Count | 12 |
| Rotatable Bond Count | 21 |
| Exact Mass | 843.386 Da |
| Monoisotopic Mass | 843.386 Da |
| Topological Polar Surface Area | 163.000 Ų |
| Heavy Atom Count | 60 |
| Formal Charge | 0 |
| Complexity | 1470.000 |
| Isotope Atom Count | 0 |
| Defined Atom Stereocenter Count | 0 |
| Undefined Atom Stereocenter Count | 1 |
| Defined Bond Stereocenter Count | 0 |
| Undefined Bond Stereocenter Count | 0 |
| The total count of all stereochemical bonds | 0 |
| Covalently-Bonded Unit Count | 1 |
| 1. Yu Chen, Shijie Bi, Xiaoli Zhang, Junjie Chen, Jianfeng Xin, Zhaonan Liu, Qing Guan, Peiju Qiu, Peng Wang, Jun Liu. (2025) Engineered probiotics remodel the intestinal epithelial barrier and enhance bacteriotherapy for inflammatory bowel diseases. Acta Biomaterialia, [PMID:40210182] [10.1016/j.actbio.2025.04.016] |
