JOE phosphoramidite, 6-isomer

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
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.

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