Molecular design of Cy3 derivative for highly sensitive in-stem molecular beacon and its application to the wash-free FISH

Bioorganic & Medicinal Chemistry
Hiromu KashidaHiroyuki Asanuma

Abstract

We herein describe a novel in-stem molecular beacon (ISMB) containing multiple Cy3-quencher pairs on d-threoninol scaffolds in the stem region. The designed Cy3 derivative was not significantly quenched by the adjacent nucleobases, self-quenching of the fluorophore was minimal, and the fluorophore did not severely destabilize the duplex. Using newly designed Cy3, we synthesized ISMBs containing two Cy3 moieties. The signal to background ratio of the ISMB containing two Cy3 moieties was above 100, whereas that with one Cy3 was 30. A Cy3-derivative containing ISMB used in a fluorescence in situ hybridization (FISH) detected endogenous β-actin mRNA in fixed cells without need for washing procedures.

References

Apr 16, 2004·Nucleic Acids Research·Philip J SantangeloGang Bao
May 10, 2005·Nucleic Acids Research·Caroline Crey-DesbiollesChristian J Leumann
May 29, 2010·Nucleic Acids Research·Antony K ChenAndrew Tsourkas

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Citations

Mar 6, 2016·Journal of Controlled Release : Official Journal of the Controlled Release Society·Mahadi HasanKentaro Kogure
Apr 9, 2015·Chembiochem : a European Journal of Chemical Biology·Keiji MurayamaHiroyuki Asanuma
Nov 24, 2016·Science and Technology of Advanced Materials·Hiromu KashidaHiroyuki Asanuma
Aug 10, 2019·Advanced Drug Delivery Reviews·Fumiaki Tomoike, Hiroshi Abe
Jul 17, 2021·Chemistry : a European Journal·Hayato KawaiHiroyuki Asanuma
Sep 18, 2021·Bioorganic & Medicinal Chemistry Letters·Kentaro TabaraTakashi Ohtsuki

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