Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag Journal Article


Authors: Dey, S. K.; Filonov, G. S.; Olarerin-George, A. O.; Jackson, B. T.; Finley, L. W. S.; Jaffrey, S. R.
Article Title: Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag
Abstract: Fluorogenic RNA aptamers are used to genetically encode fluorescent RNA and to construct RNA-based metabolite sensors. Unlike naturally occurring aptamers that efficiently fold and undergo metabolite-induced conformational changes, fluorogenic aptamers can exhibit poor folding, which limits their cellular fluorescence. To overcome this, we evolved a naturally occurring well-folded adenine riboswitch into a fluorogenic aptamer. We generated a library of roughly 1015 adenine aptamer-like RNAs in which the adenine-binding pocket was randomized for both size and sequence, and selected Squash, which binds and activates the fluorescence of green fluorescent protein-like fluorophores. Squash exhibits markedly improved in-cell folding and highly efficient metabolite-dependent folding when fused to a S-adenosylmethionine (SAM)-binding aptamer. A Squash-based ratiometric sensor achieved quantitative SAM measurements, revealed cell-to-cell heterogeneity in SAM levels and revealed metabolic origins of SAM. These studies show that the efficient folding of naturally occurring aptamers can be exploited to engineer well-folded cell-compatible fluorogenic aptamers and devices. [Figure not available: see fulltext.] © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
Keywords: mouse; animal; animals; mice; cells, cultured; embryonic stem cell; fluorescent dye; fluorescent dyes; chemistry; cell culture; embryonic stem cells; embryo, mammalian; conformation; nucleic acid conformation; genetic procedures; fluorescence imaging; aptamer; aptamers, nucleotide; optical imaging; procedures; biosensing techniques; mammalian embryo; humans; human; male
Journal Title: Nature Chemical Biology
Volume: 18
Issue: 2
ISSN: 1552-4450
Publisher: Nature Publishing Group  
Date Published: 2022-02-01
Start Page: 180
End Page: 190
Language: English
DOI: 10.1038/s41589-021-00925-0
PUBMED: 34937909
PROVIDER: scopus
PMCID: PMC8967656
DOI/URL:
Notes: Article -- Erratum issued, see DOI: 10.1038/s41589-022-00969-w -- Export Date: 1 March 2022 -- Source: Scopus
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  1. Lydia Whitney Stillman Finley
    45 Finley