Using a specific RNA-protein interaction to quench the fluorescent RNA Spinach

Laura Roszyk, Sebastian Kollenda, Sven Hennig

Research output: Contribution to JournalArticleAcademicpeer-review


RNAs are involved in interaction networks with other biomolecules and are crucial for proper cell function. Yet, their biochemical analysis remains challenging. For Förster Resonance Energy Transfer (FRET), a common tool to study such interaction networks, two interacting molecules have to be fluorescently labelled. 'Spinach' is a genetically encodable RNA aptamer, which starts to fluoresce upon binding of an organic molecule. Therefore, it is a biological fluorophore tag for RNAs. However, spinach has never been used in a FRET assembly before. Here, we describe how spinach is quenched when close to acceptors. We used RNA-DNA hybridization to bring quenchers or red organic dyes in close proximity to spinach. Furthermore, we investigate RNA-protein interactions quantitatively on the example of Pseudomonas aeruginosa phage coat protein 7 (PP7) and its interacting pp7-RNA. We utilize spinach quenching as a fully genetically encodable system even under lysate conditions. Therefore, this work represents a direct method to analyse RNA-protein interactions by quenching the spinach aptamer.

Original languageEnglish
Pages (from-to)2958-2964
Number of pages7
JournalACS chemical biology
Issue number12
Early online date23 Oct 2017
Publication statusPublished - 15 Dec 2017


  • Journal Article


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