ArticleJournal of the American Chemical Society2017
Small Molecule-Based Pattern Recognition To Classify RNA Structure.
Article in Journal of the American Chemical Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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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.
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Who cites it
28 citing papers in PubMed, 58 citations in OpenAlex.
- Cyclic Amide-Linked Oxazolidinone Triazoles as Inhibitors of the T-Box Riboswitch.Molecules (Basel, Switzerland) · 2025Article
- Mechanistic studies of small molecule ligands selective to RNA single G bulges.Nucleic acids research · 2025Article
- Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase.Nucleic acids research · 2025Article
- Expanding the recognition of monosaccharides and glycans: A comprehensive analytical approach using chemical-nose/tongue technology and a comparison to lectin microarrays.BBA advances · 2025Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer.Journal of the American Chemical Society · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- A Fluorescent Reverse-Transcription Assay to Detect Chemical Adducts on RNA.Biochemistry · 2022Article
- DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Programmable technologies to manipulate gene expression at the RNA level.Current opinion in chemical biology · 2021Review
- Recognition of single-stranded nucleic acids by small-molecule splicing modulators.Nucleic acids research · 2021Article
- Selective discrimination and classification of G-quadruplex structures with a host-guest sensing array.Nature chemistry · 2021Article
- Targeting RNA with small molecules: from fundamental principles towards the clinic.Chemical Society reviews · 2021Review
- Small molecule-RNA targeting: starting with the fundamentals.Chemical communications (Cambridge, England) · 2020Article
- Design of small molecules targeting RNA structure from sequence.Chemical Society reviews · 2020Review
- RNA drug discovery: Conformational restriction enhances specific modulation of the T-box riboswitch function.Bioorganic & medicinal chemistry · 2020Article
- Systematic analysis of the interactions driving small molecule-RNA recognition.RSC medicinal chemistry · 2020Article
- NMR characterization of RNA small molecule interactions.Methods (San Diego, Calif.) · 2019Review
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules.Journal of the American Chemical Society · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes. Complete (100%) predictive ability for this RNA training set was achieved by incorporating two exhaustively guanidinylated aminoglycosides into the receptor library. The PCA was then externally validated using biologically relevant RNA constructs. In bulge-stem-loop constructs of HIV-1 transactivation response element (TAR) RNA, we achieved nucleotide-specific classification of two independent secondary structure motifs. Furthermore, examination of cheminformatic parameters and PCA loading factors revealed trends in aminoglycoside:RNA recognition, including the importance of shape-based discrimination, and suggested the potential for size and sequence discrimination within RNA structural motifs. These studies present a new approach to classifying RNA structure and provide direct evidence that RNA topology, in addition to sequence, is critical for the molecular recognition of RNA.
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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.