TAMRA phosphoramidite, 5-isomer

Product Introduction

This phosphoramidite is used for synthesis of oligonucleotides 5’-labeled with TAMRA.,TAMRA
(carboxytetramethylrhodamine) is a xanthene dye from the rhodamine family with emission in the orange
spectrum range (maximum at 563 nm). This fluorophore is traditionally used as a FRET-acceptor
(and a quencher) in a pair with fluorescein (FAM) due to significant overlapping of their
spectra. Thus, this phosphoramidite is convenient for the synthesis of dual-labeled probes TaqMan, which
contain 5’-terminal TAMRA and FAM in the middle of the sequence or at the 3’-end
(using Fluorescein dT Phosphoramidite and FAM
CPG, respectively).,TAMRA 5’-labeled oligonucleotides are commonly used for quantitative PCR
and fragment analysis (for example, for microsatellite marker analysis) because the equipment available has a detection
channel for TAMRA frequently.,The TAMRA dye is not stable in the presence of ammonium and
sterically non-hindered primary amines, so it is strongly recommended to follow specified
conditions for labeled oligonucleotide deprotection.,Coupling: 7.5 min.,Deprotection: tret-buthylamine : methanol : water 1 : 1 : 3 (v/v/v) («TAMRA cocktail») for 6 hours at 60 °C, then cool down to room temperature.,Due to complete and irreversible degradation of the TAMRA dye, do NOT use aqueous ammonium and AMA for deprotecting a modified oligonucleotide from the solid-phase support.

Chemical Information
Purity	NMR 1H, HPLC-MS (95%), coupling test
IUPAC Name	N-[4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxycyclohexyl]-3',6'-bis(dimethylamino)-3-oxospiro[2-benzofuran-1,9'-xanthene]-5-carboxamide
Canonical SMILES	CC(C)N(C(C)C)P(OCCC#N)OC1CCC(CC1)NC(=O)C2=CC3=C(C=C2)C4(C5=C(C=C(C=C5)N(C)C)OC6=C4C=CC(=C6)N(C)C)OC3=O
InChI	InChI=1S/C40H50N5O6P/c1-25(2)45(26(3)4)52(48-21-9-20-41)51-31-15-11-28(12-16-31)42-38(46)27-10-17-33-32(22-27)39(47)50-40(33)34-18-13-29(43(5)6)23-36(34)49-37-24-30(44(7)8)14-19-35(37)40/h10,13-14,17-19,22-26,28,31H,9,11-12,15-16,21H2,1-8H3,(H,42,46)
InChI Key	ZHZWFIMSTLVPMN-UHFFFAOYSA-N
Solubility	Good in acetonitrile, dichloromethane
Appearance	Purple solid

Computed Properties
XLogP3	6.3
Hydrogen Bond Donor Count	1
Hydrogen Bond Acceptor Count	10
Rotatable Bond Count	12
Exact Mass	727.34987133 g/mol
Monoisotopic Mass	727.34987133 g/mol
Topological Polar Surface Area	117Ų
Heavy Atom Count	52
Formal Charge	0
Complexity	1240
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