title: Solid- and solution-phase synthesis and application of R6G dual-labeled oligonucleotide probes.
abstract: A novel N-TFA-protected carboxyrhodamine 6G (R6G) phosphoramidite was synthesized for use in an automated DNA synthesis to prepare 5'-labeled oligonucleotides. Deprotection and purification conditions were optimized for 5'-labeled and dual-labeled oligonucleotide probes. As an alternative we synthesized an azide derivative of R6G for CuAAC post-synthetic oligonucleotide labeling. Dual-labeled probes obtained by both methods showed the same efficacy in a quantitative PCR assay. R6G-labeled probes demonstrated superior properties in a qPCR assay in comparison with alternative HEX, JOE and SIMA dyes due to more efficient fluorescence quenching by BHQ-1. We successfully used R6G dual-labeled probes for rotavirus genotyping.
authors.affiliation: Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
authors.forename: Aleksander Yu
authors.initials: AY
authors.lastname: Skoblov
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: Maxim V
authors.initials: MV
authors.lastname: Vichuzhanin
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: Valentina M
authors.initials: VM
authors.lastname: Farzan
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: Olga A
authors.initials: OA
authors.lastname: Veselova
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Konovalova
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: Alexander T
authors.initials: AT
authors.lastname: Podkolzin
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia.
authors.forename: German A
authors.initials: GA
authors.lastname: Shipulin
authors.affiliation: Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119992, Russia; Skolkovo Institute of Science and Technology, 5 Innovation Center "Skolkovo", Skolkovo 143026, Russia. Electronic address: t.zatsepin@skoltech.ru.
authors.forename: Timofei S
authors.initials: TS
authors.lastname: Zatsepin
mesh_terms: D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry; D005838:Genotype; D015345:Oligonucleotide Probes / Q000138:chemical synthesis* / Q000737:chemistry*; D012235:Rhodamines / Q000737:chemistry*; D012401:Rotavirus / Q000235:genetics; D012996:Solutions
chemical_list: D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D012235:Rhodamines; D012996:Solutions; C026188:rhodamine 6G
keywords: CuAAC; Fluorescent dye; Oligonucleotide; Phosphoramidite; Rhodamine 6G; qPCR