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R6G phosphoramidite, 6-isomer | CAS 1355330-47-0
| Catalog Number | A19-0094 |
| Category | DNA Stains |
| Molecular Formula | C46H54F6N5O8P |
| Molecular Weight | 949.93 |
* Please be kindly noted products are not for therapeutic use. We do not sell to patients.
Product Introduction
R6G phosphoramidite for oligonucleotide synthesis, pure 6-isomer.,R6G (rhodamine 6G) is a xanthene dye of the rhodamine family with high fluorescence quantum yield and high molar extinction coefficient. Relative to those of fluorescein, the absorption (518 nm) and emission (542 nm) maxima of 6-R6G are shifted into the long-wave region.,R6G can be used as a FRET acceptor in DNA-sequencing and in short tandem repeat (STR) analysis. The dye is commonly used for producing TaqMan probes for quantitative PCR. In comparison with HEX and JOE dyes, R6G in combination with BHQ1 quencher has stronger quenching in molecular beacon probes, significantly reducing background fluorescence in PCR.,Coupling: 10 minutes.,Deprotection: solution of tert-Butylamine in water (1:3 v/v) overnight at 55°С.,Aqueous ammonia and AMA (solution of 30% ammonium hydroxide/40% aqueous methylamine 1:1 v/v) must NOT be used for deprotection of the modified oligonucleotide from the solid-phase support because of complete and irreversible R6G degradation.
Chemical Information
Product Specification
Computed Properties
Patents
| Synonyms | N-[6-[[(2-Cyanoethoxy)](diisopropylamino)phosphinooxy]hexyl]-3-oxo-3',6'-bis[ethyl(trifluoroacetyl)amino]-2',7'-dimethylspiro[isobenzofuran-1(3H),9'-[9H]xanthene]-6-carboxamide |
| Purity | NMR 1H and 31P, HPLC-MS (95+%), isomeric purity > 97% |
| IUPAC Name | N-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexyl]-3',6'-bis[ethyl-(2,2,2-trifluoroacetyl)amino]-2',7'-dimethyl-1-oxospiro[2-benzofuran-3,9'-xanthene]-5-carboxamide |
| Canonical SMILES | CCN(C1=CC2=C(C=C1C)C3(C4=C(O2)C=C(C(=C4)C)N(CC)C(=O)C(F)(F)F)C5=C(C=CC(=C5)C(=O)NCCCCCCOP(N(C(C)C)C(C)C)OCCC#N)C(=O)O3)C(=O)C(F)(F)F |
| InChI | InChI=1S/C46H54F6N5O8P/c1-9-55(42(60)45(47,48)49)36-25-38-34(22-29(36)7)44(35-23-30(8)37(26-39(35)64-38)56(10-2)43(61)46(50,51)52)33-24-31(16-17-32(33)41(59)65-44)40(58)54-19-13-11-12-14-20-62-66(63-21-15-18-53)57(27(3)4)28(5)6/h16-17,22-28H,9-15,19-21H2,1-8H3,(H,54,58) |
| InChIKey | RKEJFZFXKNKKCI-UHFFFAOYSA-N |
| Solubility | Good in DCM, acetonitrile |
| Appearance | Yellowish foam |
| CF260 | 0.18 |
| CF280 | 0.17 |
| Fluorescence Quantum Yield | 0.95 |
| Excitation | 518 |
| Emission | 542 |
| Storage | Storage: 12 months after receival at -20 °C in the Dark. Transportation: at room temperature for up to 2 weeks. Avoid prolonged exposure to light. Desiccate. |
| XLogP3 | 8.6 |
| Hydrogen Bond Donor Count | 1 |
| Hydrogen Bond Acceptor Count | 16 |
| Rotatable Bond Count | 19 |
| Exact Mass | 949.36141967 g/mol |
| Monoisotopic Mass | 949.36141967 g/mol |
| Topological Polar Surface Area | 151Ų |
| Heavy Atom Count | 66 |
| Formal Charge | 0 |
| Complexity | 1660 |
| 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 |
| Publication Number | Title | Priority Date |
|---|---|---|
| US-2012016128-A1 | Rhodamine lactone phosphoramidites and polymers | 2010-07-16 |
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