ArticleNature chemical biology2021
Structure-based investigation of fluorogenic Pepper aptamer.
Article in Nature chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed, 85 citations in OpenAlex.
- Fluorogenic RNA aptamers in cancer: emerging platforms for molecular imaging, biosensing, and precision oncology.Molecular biology reports · 2026Review
- Nitro Reduction-Based RNA Control and Ultrafast Release.Angewandte Chemie (International ed. in English) · 2026Article
- Application of Pepper aptamer-based reporter system for bacterial transcription studies.Archives of microbiology · 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
- Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform.Nature communications · 2026Article
- NirFAP680: a highly bright and stable large Stokes shift near-infrared fluorogen-activating protein.Nature methods · 2026Article
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.Chemical & biomedical imaging · 2026Review
- Programmable fluorescent aptamer-based RNA switches for rapid identification of point mutations.Nature chemistry · 2025Article
- Structural and functional clues challenge the hypothesis that the yjdF riboswitch is natively regulated through broad recognition of azaaromatic compounds.Nucleic acids research · 2025Article
- Advancing Single-Molecule Biophysics: Next-Generation Organic Fluorophores with Tailored Labeling Strategies.Chemical & biomedical imaging · 2025Review
- Structural basis and affinity improvement for an ATP-binding DNA aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structure-based insights into the ligand specificity tuning of 2'-dG-III riboswitch.Nucleic acids research · 2025Article
- Structure-informed design of an ultrabright RNA-activated fluorophore.Nature chemistry · 2025Article
- Engineering covalent small molecule-RNA complexes in living cells.Nature chemical biology · 2025Article
- Peri-centrosomal localization of small interfering RNAs in C. elegans.Science China. Life sciences · 2025Article
- Article
- 1000 fold Ultra-Photosensitized Fluorescent Protein Mimics Toward Photocatalytic Proximity Labeling and Proteomic Profiling Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.