6-JOE phosphoramidite

Catalog number: BRP-02237

6-JOE phosphoramidite

6-JOE phosphoramidite is a fluorescent dye used for oligonucleotide labeling.

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Catalog
BRP-02237
Synonyms
6-(4',5'-Dichloro-2',7'-dimethoxy-3',6'-dipivaloylfluorescein-6-carboxamido)-hexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite; 5'-Dichloro-dimethoxy-Fluorescein Phosphoramidite II (Joe II); JOE phosphoramidite, 6-isomer; 5-Carboxy-2',7'-dimethoxy-4',5'-dichloro-fluoresceinamide phosphoramidite; 4',5'-dichloro-6-((6-(((2-cyanoethoxy)(diisopropylamino)phosphaneyl)oxy)hexyl)carbamoyl)-2',7'-dimethoxy-3-oxo-3H-spiro[isobenzofuran-1,9'-xanthene]-3',6'-diyl bis(2,2-dimethylpropanoate)
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
Molecular Weight
972.88
Molecular Formula
C48H60Cl2N3O12P
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)
InChIKey
CKBMUCQWGUZAKQ-UHFFFAOYSA-N
Purity
≥95%
Solubility
Soluble in Anhydrous Acetonitrile
Appearance
White solid
Storage
Store at -20 °C
Absorption Maximum (Lambda Max)
533
Fluorescence Maximum
554

Chemical Structure:

Reference Reading

1. Improved Synthesis of Phosphoramidite-Protected N6-Methyladenosine via BOP-Mediated SNAr Reaction
Shifali Shishodia, Christopher J Schofield. Molecules. 2020 Dec 31;26(1):147. doi: 10.3390/molecules26010147.
N6-methyladenosine(m6A) is the most abundant modification in mRNA. Studies on proteins that introduce and bind m6A require the efficient synthesis of oligonucleotides containing m6A. We report an improved five-step synthesis of the m6A phosphoramidite starting from inosine, utilising a 1-H-benzotriazol-1-yloxytris(dimethylamino)phosphoniumhexafluorophosphate (BOP)-mediated SNAr reaction in the key step. The route manifests a substantial increase in overall yield compared to reported routes, and is useful for the synthesis of phosphoramidites of other adenosine derivatives, such as ethanoadenosine, an RNA analogue of the DNA adduct formed by the important anticancer drug Carmustine.
2. Catalytic asymmetric and stereodivergent oligonucleotide synthesis
Aaron L Featherston, Yongseok Kwon, Matthew M Pompeo, Oliver D Engl, David K Leahy, Scott J Miller. Science. 2021 Feb 12;371(6530):702-707. doi: 10.1126/science.abf4359.
We report the catalytic stereocontrolled synthesis of dinucleotides. We have demonstrated, for the first time to our knowledge, that chiral phosphoric acid (CPA) catalysts control the formation of stereogenic phosphorous centers during phosphoramidite transfer. Unprecedented levels of diastereodivergence have also been demonstrated, enabling access to either phosphite diastereomer. Two different CPA scaffolds have proven to be essential for achieving stereodivergence: peptide-embedded phosphothreonine-derived CPAs, which reinforce and amplify the inherent substrate preference, and C2-symmetric BINOL-derived CPAs, which completely overturn this stereochemical preference. The presently reported catalytic method does not require stoichiometric activators or chiral auxiliaries and enables asymmetric catalysis with readily available phosphoramidites. The method was applied to the stereocontrolled synthesis of diastereomeric dinucleotides as well as cyclic dinucleotides, which are of broad interest in immuno-oncology as agonists of the stimulator of interferon genes (STING) pathway.
3. On-demand synthesis of phosphoramidites
Alexander F Sandahl, Thuy J D Nguyen, Rikke A Hansen, Martin B Johansen, Troels Skrydstrup, Kurt V Gothelf. Nat Commun. 2021 May 12;12(1):2760. doi: 10.1038/s41467-021-22945-z.
Automated chemical synthesis of oligonucleotides is of fundamental importance for the production of primers for the polymerase chain reaction (PCR), for oligonucleotide-based drugs, and for numerous other medical and biotechnological applications. The highly optimised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the phosphate precursors and one of the drawbacks of this technology is the poor bench stability of phosphoramidites. Here, we report on the development of an on-demand flow synthesis of phosphoramidites from their corresponding alcohols, which is accomplished with short reaction times, near-quantitative yields and without the need of purification before being submitted directly to automated oligonucleotide synthesis. Sterically hindered as well as redox unstable phosphoramidites are synthesised using this methodology and the subsequent couplings are near-quantitative for all substrates. The vision for this technology is direct integration into DNA synthesisers thereby omitting manual synthesis and storage of phosphoramidites.
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