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Molecular Beacon DNA Probes with Fluorescein Bifluorophore.

ABSTRACT: An azido-derivative of a fluorescein bifluorophore was obtained and used for the synthesis of "molecular beacon"-type oligonucleotide fluorogenic probes for RT-PCR. Eight probe variants were synthesized based on an optimized sequence: with one or two quencher residues at the 3'-end, with a single or bifluorophore fluorescein label attached to 5'-end using modifying phosphoramidites (short linker) or "click reaction" (long linker). Comparison of probes in RT-PCR showed that probes with a doubled quencher (single fluorescein on a short linker) and doubled dye on a short linker (single dye) are somewhat superior in sensitivity to a standard probe (single quencher, single dye on a short linker) by the value of ΔC_t = 1-2.

Supplementary information

The online version contains supplementary material available at 10.1134/S1068162021030055.

SUBMITTER: Brylev VA

PROVIDER: S-EPMC8193957 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Molecular Beacon DNA Probes with Fluorescein Bifluorophore.

Brylev V A VA Lysenko I L IL Kokin E A EA Martynenko-Makaev Y V YV Ryazantsev D Y DY Shmanai V V VV Korshun V A VA

Russian journal of bioorganic chemistry 20210611 3

An azido-derivative of a fluorescein bifluorophore was obtained and used for the synthesis of "molecular beacon"-type oligonucleotide fluorogenic probes for RT-PCR. Eight probe variants were synthesized based on an optimized sequence: with one or two quencher residues at the 3'-end, with a single or bifluorophore fluorescein label attached to 5'-end using modifying phosphoramidites (short linker) or "click reaction" (long linker). Comparison of probes in RT-PCR showed that probes with a doubled ...[more]

PMID: 34149274

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