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Updated: Feb 15, 2026

Detection of Viral RNA by Fluorescence in situ Hybridization FISH
Published on: May 5, 2012
Detecting Circular RNAs by RNA Fluorescence In Situ Hybridization
Anne Zirkel1, Argyris Papantonis2
1Chromatin Systems Biology Laboratory, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
Abstract:
Fluorescence in situ hybridization (FISH) coupled to high-resolution microscopy is a powerful method for analyzing the subcellular localization of RNA. However, the detection of circular RNAs (circRNAs) using microscopy is challenging because the only feature of a circRNA that can be used for the probe design is its junction. Circular RNAs are expressed at varying levels, and for their efficient monitoring by FISH, background fluorescence levels need to be kept low. Here, we describe a FISH protocol coupled to high-precision localizations using a single fluorescently labeled probe spanning the circRNA junction; this allows circRNA detection in mammalian cells with high signal-to-noise ratios.
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