ArticleNucleic acids research2023
Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- Application of Pepper aptamer-based reporter system for bacterial transcription studies.Archives of microbiology · 2026Article
- Aptamer-based DNA nanoswitches for multiplexed protein detection.Chemical communications (Cambridge, England) · 2026Article
- Live-cell imaging of RNA dynamics using bright and stable fluorescent RNAs.Nature protocols · 2026Review
- Honeydew: A Fluorescent Aptamer for Low-Cost Azo Food Dyes.Chembiochem : a European journal of chemical biology · 2026Article
- Cyclic transformation of stable/metastable nucleic acid structures enables dynamic monitoring of ATP in living cells.Chemical science · 2026Article
- A versatile method for designing biosensors via regulatory domains of allosteric enzymes.Nature communications · 2026Article
- Aptamer-based DNA nanoswitches for multiplexed protein detection.bioRxiv : the preprint server for biology · 2026Article
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- Real-Time and Spatially Resolved Epigenetic Dynamics Tracking Beyond DNA Methylation via Live-Cell Epigenetic Sensors in 3D Systems.Biosensors · 2026Review
- Engineering ligands for theophylline riboswitches expands its regulatory dynamic range in prokaryotic and eukaryotic systems.Nature communications · 2026Article
- Characterizing Cell-Free Transcription and Translation Dynamics with Nucleic Acid-Based Assays.ACS synthetic biology · 2026Article
- Structure-based insights into the ligand specificity tuning of 2'-dG-III riboswitch.Nucleic acids research · 2025Article
- Specific Targeting and Imaging of RNA G-Quadruplex (rG4) Structure Using Non-G4-Containing l-RNA Aptamer and Fluorogenic l-Aptamer.Small methods · 2025Article
- Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells.Journal of the American Chemical Society · 2025Article
- Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes.Nucleic acids research · 2025Article
- Near-infrared fluorogenic RNA for in vivo imaging and sensing.Nature communications · 2025Article
- Artificial dynamic structure ensemble-guided rational design of a universal RNA aptamer-based sensing tag.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives.Biosensors · 2024Review
- Investigating the Effect of RNA Scaffolds on the Multicolor Fluorogenic Aptamer Pepper in Different Bacterial Species.ACS synthetic biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sensors to measure the abundance and signaling of intracellular molecules are crucial for understanding their physiological functions. Although conventional fluorescent protein-based sensors have been designed, RNA-based sensors are promising imaging tools. Numerous RNA-based sensors have been developed. These sensors typically contain RNA G-quadruplex (RG4) motifs and thus may be suboptimal in living cells. Here we describe RNA-based sensors based on Pepper, a fluorogenic RNA without an RG4 motif. With Pepper, we engineered various sensors for metabolites, synthetic compounds, proteins and metal ions in vitro and in living cells. In addition, these sensors show high activation and selectivity, demonstrating their universality and robustness. In the case of sensors responding to S-adenosylmethionine (SAM), a metabolite produced by methionine adenosyltransferase (MATase), we showed that our sensors exhibited positively correlated fluorescence responding to different SAM levels. Importantly, we revealed the SAM biosynthesis pathway and monitored MATase activity and gene expression spatiotemporally in living individual human cells. Additionally, we constructed a ratiometric SAM sensor to determine the inhibition efficacy of a MATase inhibitor in living cells. Together, these sensors comprising Pepper provide a useful platform for imaging diverse cellular targets and their signaling pathway.
Indexed as
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.