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Updated: Feb 15, 2026

Detection of Viral RNA by Fluorescence in situ Hybridization FISH
Published on: May 5, 2012
Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as
Christine Kocks1, Anastasiya Boltengagen2, Monika Piwecka2
1Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany. christine.kocks@mdc-berlin.de.
Abstract:
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.
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