title: Non-nucleoside phosphoramidites of xanthene dyes (FAM, JOE, and TAMRA) for oligonucleotide labeling.
abstract: This unit describes the preparation of 5- and 6-carboxy derivatives of the xanthene fluorescent dyes fluorescein (FAM), 4',5'-dichloro-2',7'-dimethoxy-fluorescein (JOE), and tetramethylrhodamine (TAMRA) as individual isomers, and their conversion to non-nucleoside phosphoramidite reagents suitable for oligonucleotide labeling. The use of a cyclohexylcarbonyl (Chc) protecting group for blocking of phenolic hydroxyls facilitates the chromatographic separation of isomers of carboxy-FAM and carboxy-JOE as pentafluorophenyl esters. Acylation of 3-dimethylaminophenol with 1,2,4-benzenetricarboxylic anhydride gave a mixture of 4-dimethylamino-2-hydroxy-2',4'(5')-dicarboxybenzophenones, easily separable into individual compounds upon fractional crystallization. Individual isomeric benzophenones are precursors of 5- or 6-carboxytetramethylrhodamines. The dyes were converted into 6-aminohexanol- (JOE), 4-trans-aminocyclohexanol- (FAM and JOE), and hydroxyprolinol-based (TAMRA) phosphoramidite reagents.
authors.affiliation: Institute of Physical Organic Chemistry, Minsk, Belarus.
authors.forename: Maksim V
authors.initials: MV
authors.lastname: Kvach
authors.affiliation: Institute of Physical Organic Chemistry, Minsk, Belarus.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Tsybulsky
authors.affiliation: Institute of Physical Organic Chemistry, Minsk, Belarus.
authors.forename: Vadim V
authors.initials: VV
authors.lastname: Shmanai
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Prokhorenko
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
authors.forename: Irina A
authors.initials: IA
authors.lastname: Stepanova
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Korshun
mesh_terms: D000627:Aminophenols / Q000737:chemistry; D005452:Fluoresceins / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D017665:Hydroxyl Radical; D007202:Indicators and Reagents / Q000737:chemistry; D007536:Isomerism; D009841:Oligonucleotides / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry; D012235:Rhodamines / Q000737:chemistry*; D014966:Xanthenes / Q000737:chemistry
chemical_list: D000627:Aminophenols; D005452:Fluoresceins; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D012235:Rhodamines; D014966:Xanthenes; C434331:phosphoramidite; D017665:Hydroxyl Radical; C005358:tetramethylrhodamine; C007465:3-dimethylaminophenol