ArticleNature computational science2024
Deep generative design of RNA aptamers using structural predictions.
Article in Nature computational science, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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.
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Who cites it
32 citing papers in PubMed.
- Molecular Engineering of Aptamers for Glioblastoma Therapy: From Simple Antagonists to AI-Driven Approaches, a Narrative Review.International journal of molecular sciences · 2026Review
- Nucleic acid aptamers: new methods for selection, target validation, molecular diagnostics and therapeutics.Signal transduction and targeted therapy · 2026Review
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform.Nature communications · 2026Article
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- Artificial intelligence in biologic drug discovery: A review of methodological evolution and therapeutic applications.Acta pharmaceutica Sinica. B · 2026Review
- Generalist biological artificial intelligence in modeling the language of life.Nature biotechnology · 2026Review
- High-throughput engineering of ligand-activated splicing ribozyme through domain insertion.bioRxiv : the preprint server for biology · 2026Article
- Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.Nucleic acids research · 2026Article
- Lifetime-based multiplexed detection of viral RNA using fluorogenic aptamers.bioRxiv : the preprint server for biology · 2026Article
- De novo design of functional nucleic acids of aptamers.Nature computational science · 2026Article
- Iterative design of a NAND hybrid riboswitch by deep batch Bayesian optimization.Nucleic acids research · 2026Article
- Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.Chemical & biomedical imaging · 2026Review
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Accessory microRNA byproducts expand RNA interference via microprocessor-mediated cleavage activation.Science advances · 2026Article
- Single-round evolution of RNA aptamers with GRAPE-LM.Nature biotechnology · 2026Article
- Harnessing deep learning to accelerate the development of antibodies and aptamers.Acta pharmaceutica Sinica. B · 2026Review
- PyFuRNAce: an integrated design engine for RNA origami.Nature communications · 2025Article
- Generating functional plasmid origins with OriGen.Nucleic acids research · 2025Article
- Mechanomedicine: Present state and future promise.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
RNAs represent a class of programmable biomolecules capable of performing diverse biological functions. Recent studies have developed accurate RNA three-dimensional structure prediction methods, which may enable new RNAs to be designed in a structure-guided manner. Here, we develop a structure-to-sequence deep learning platform for the de novo generative design of RNA aptamers. We show that our approach can design RNA aptamers that are predicted to be structurally similar, yet sequence dissimilar, to known light-up aptamers that fluoresce in the presence of small molecules. We experimentally validate several generated RNA aptamers to have fluorescent activity, show that these aptamers can be optimized for activity in silico, and find that they exhibit a mechanism of fluorescence similar to that of known light-up aptamers. Our results demonstrate how structural predictions can guide the targeted and resource-efficient design of new RNA sequences.
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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.