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Rink MR, Baptista MAP, Flomm FJ, Hennig T, Whisnant AW, Wolf N, Seibel J, Dölken L, Bosse JB. Concatemeric Broccoli reduces mRNA stability and induces aggregates. PLoS One 2021; 16:e0244166. [PMID: 34347781 PMCID: PMC8336797 DOI: 10.1371/journal.pone.0244166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/17/2021] [Indexed: 11/18/2022] Open
Abstract
Fluorogenic aptamers are an alternative to established methodology for real-time imaging of RNA transport and dynamics. We developed Broccoli-aptamer concatemers ranging from 4 to 128 substrate-binding site repeats and characterized their behavior fused to an mCherry-coding mRNA in transient transfection, stable expression, and in recombinant cytomegalovirus infection. Concatemerization of substrate-binding sites increased Broccoli fluorescence up to a concatemer length of 16 copies, upon which fluorescence did not increase and mCherry signals declined. This was due to the combined effects of RNA aptamer aggregation and reduced RNA stability. Unfortunately, both cellular and cytomegalovirus genomes were unable to maintain and express high Broccoli concatemer copy numbers, possibly due to recombination events. Interestingly, negative effects of Broccoli concatemers could be partially rescued by introducing linker sequences in between Broccoli repeats warranting further studies. Finally, we show that even though substrate-bound Broccoli is easily photobleached, it can still be utilized in live-cell imaging by adapting a time-lapse imaging protocol.
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Affiliation(s)
- Marco R. Rink
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy University of Birmingham, Birmingham, United Kingdom
| | - Marisa A. P. Baptista
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Felix J. Flomm
- Centre for Structural Systems Biology, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover Medical School, Hannover, Germany
- Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Natalia Wolf
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Jens B. Bosse
- Centre for Structural Systems Biology, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover Medical School, Hannover, Germany
- Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- * E-mail:
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