title: Molecular beacons with JOE dye: Influence of linker and 3' couple quencher.
abstract: Molecular beacons carrying JOE dye (4',5'-dichloro-2',7'-dimethoxy-6-carboxyfluorescein) on a rigid or flexible linker and one or two BHQ1 quenchers have been prepared and tested in real-time PCR using Fusarium avenaceum elongation factor 1α DNA template. The probes were different in their structures (loop size and stem length), linkers for dye attachment (6-aminohexanol or trans-4-aminocyclohexanol), quencher composition (single and double BHQ1) to elucidate the influence of all these features. Fluorogenic properties of the probes were studied and compared to those of FAM (fluorescein)-based probes. All the factors - stem length, JOE vs FAM, rigid vs flexible linker, single vs double quencher - appeared to play a considerable role in the probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Institute of Physical Organic Chemistry, 220072, Minsk, Belarus.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Tsybulsky
authors.affiliation: Institute of Physical Organic Chemistry, 220072, Minsk, Belarus.
authors.forename: Maksim V
authors.initials: MV
authors.lastname: Kvach
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
authors.forename: Dmitry Y
authors.initials: DY
authors.lastname: Ryazantsev
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia. Electronic address: aparinmgu@mail.ru.
authors.forename: Ilya O
authors.initials: IO
authors.lastname: Aparin
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Stakheev
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Gause Institute of New Antibiotics, 119021, Moscow, Russia.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Prokhorenko
authors.affiliation: Institute of Physical Organic Chemistry, 220072, Minsk, Belarus.
authors.forename: Yury V
authors.initials: YV
authors.lastname: Martynenko
authors.affiliation: Primetech LLC, 220072, Minsk, Belarus.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Gontarev
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Formanovsky
authors.affiliation: Central Research Institute of Epidemiology, 111123, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 119992, Moscow, Russia; Skolkovo Institute of Science and Technology, 143026, Skolkovo, Russia.
authors.forename: Timofei S
authors.initials: TS
authors.lastname: Zatsepin
authors.affiliation: Institute of Physical Organic Chemistry, 220072, Minsk, Belarus.
authors.forename: Vadim V
authors.initials: VV
authors.lastname: Shmanai
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Gause Institute of New Antibiotics, 119021, Moscow, Russia.
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Korshun
authors.affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia. Electronic address: szavriev@ibch.ru.
authors.forename: Sergey K
authors.initials: SK
authors.lastname: Zavriev
mesh_terms: D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics; D005452:Fluoresceins / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D015335:Molecular Probes / Q000737:chemistry*; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction; D012015:Reference Standards; D013696:Temperature; D014966:Xanthenes / Q000737:chemistry
chemical_list: C572521:4',5'-dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein; D015342:DNA Probes; D005452:Fluoresceins; D005456:Fluorescent Dyes; D015335:Molecular Probes; D014966:Xanthenes
keywords: Couple quencher; JOE dye; Linkers; Molecular beacons; Real-time PCR