R6G phosphoramidite, 6-isomer | 1355330-47-0

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
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)
InChI Key	RKEJFZFXKNKKCI-UHFFFAOYSA-N
Solubility	Good in DCM, acetonitrile
Appearance	Yellowish foam

Product Specification
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.

Computed Properties
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

Patents

Publication Number	Title	Priority Date
US-2012016128-A1	Rhodamine lactone phosphoramidites and polymers	2010-07-16