ArticleNature nanotechnology2019
Computational design of three-dimensional RNA structure and function.
Article in Nature nanotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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Who cites it
44 citing papers in PubMed, 72 citations in OpenAlex.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Destabilization of Structured RNAs by OPC and TIP4PD Water Models.Journal of chemical theory and computation · 2026Article
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- Article
- RNA adapts its flexibility to efficiently fold and resist unfolding.Nucleic acids research · 2025Article
- gRNAde: Geometric Deep Learning for 3D RNA inverse design.bioRxiv : the preprint server for biology · 2025Article
- gRNAde: A Geometric Deep Learning Pipeline for 3D RNA Inverse Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Machine Learning for RNA Design: LEARNA.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.Nucleic acids research · 2024Article
- High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping.Nucleic acids research · 2024Article
- Therapeutic applications of RNA nanostructures.RSC advances · 2024Review
- Ribonanza: deep learning of RNA structure through dual crowdsourcing.bioRxiv : the preprint server for biology · 2024Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.ACS synthetic biology · 2023Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.bioRxiv : the preprint server for biology · 2023Article
- Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions.Journal of molecular biology · 2023Article
- Nucleic acid nanostructures forApplied physics reviews · 2023Review
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 1 country.
Funding
Abstract
RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.
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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.