Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer.

Regina Wirth, Peng Gao, G Ulrich Nienhaus, Murat Sunbul, Andres Jäschke

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Article in Bio-protocol, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Development of label-free light-controlled gene expression technologies using mid-IR and terahertz light.Frontiers in bioengineering and biotechnology · 2024
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5 · Who and what money

Authors and funding

5 authors.

Regina WirthInstitute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany.

Peng GaoInstitute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.

G Ulrich NienhausInstitute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.

Murat SunbulInstitute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany.

Andres JäschkeInstitute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be compatible with advanced super-resolution techniques, mainly due to poor photophysical properties of their small-molecule fluorogens. Here, we describe a detailed protocol for fluorescence microscopy of mRNA in live bacteria using the recently reported fluorogenic silicon rhodamine binding aptamer (SiRA) featuring excellent photophysical properties. Notably, with SiRA, we demonstrated the first aptamer-based RNA visualization using super-resolution (STED) microscopy. This imaging method can be especially valuable for visualization of RNA in prokaryotes since the size of a bacterium is only a few times greater than the optical resolution of a conventional microscope.

Indexed as

Confocal fluorescence microscopyLight-up aptamerLive cell imagingRNA imagingSilicon rhodamineSiRA aptamerSTED microscopy

Identifiers

PMID33659569

DOI10.21769/BioProtoc.3603

PMCPMC7842314

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.