Automated One-Double-Z Pair BaseScope™ for CircRNA In Situ Hybridization

Boye Schnack Nielsen*, Trine Møller, Jørgen Kjems

*Corresponding author for this work

Research output: Contribution to book/anthology/report/proceedingBook chapterResearchpeer-review


Circular RNAs (circRNAs) are single-stranded RNA, typically exons, connected head to tail by back-splicing. The functions of circRNAs include binding of microRNA, regulation of transcription, regulation of alternative splicing, and modulation of immune response. As for other RNA transcripts their levels vary during development and may also become deregulated during disease progression. Different from linear RNAs, the circRNAs are not susceptible to traditional exonuclease activity and therefore more stable in tissues and blood. This makes the circRNAs an attractive new group of potential biomarkers. Specific detection of circRNAs in situ is challenged by the need to discriminate bona fide circRNAs from the linear precursor forms and splice variants that contain largely overlapping sequences. Knowing the sequence around the splice junction site makes the branched DNA probe technology, BaseScope, suitable for selective detection of unique circRNAs. Here, we present the automated application of BaseScope with a one-double-Z pair probe set designed for the junction of circHIPK3.

Original languageEnglish
Title of host publication In Situ Hybridization Protocols
EditorsBoye Schnack Nielsen, Julia Jones
Number of pages10
Place of publicationNew York
PublisherHumana Press, Inc.
Publication date2020
ISBN (Print)978-1-0716-0622-3
ISBN (Electronic)978-1-0716-0623-0
Publication statusPublished - 2020
SeriesMethods in Molecular Biology


  • Automation
  • BaseScope
  • circHIPK3
  • circRNA
  • In situ hybridization
  • Ventana


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