Molecular beacons with JOE dye: Influence of linker and 3′ couple quencher

Dmitry A. Tsybulsky, Maksim V. Kvach, Dmitry Y. Ryazantsev, Ilya O. Aparin, Alexander A. Stakheev, Igor A. Prokhorenko, Yury V. Martynenko, Sergey V. Gontarev, Andrey A. Formanovsky, Timofei S. Zatsepin, Vadim V. Shmanai, Vladimir A. Korshun, Sergey K. Zavriev

    Research output: Contribution to journalArticlepeer-review

    4 Citations (Scopus)


    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).

    Original languageEnglish
    Pages (from-to)285-290
    Number of pages6
    JournalMolecular and Cellular Probes
    Issue number5
    Publication statusPublished - 1 Oct 2016


    • Couple quencher
    • JOE dye
    • Linkers
    • Molecular beacons
    • Real-time PCR


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