ArticleNucleic acids research2014
Complete RNA inverse folding: computational design of functional hammerhead ribozymes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- SamplingDesign: RNA design via continuous optimization with coupled variables and Monte-Carlo sampling.Nature communications · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Computational De Novo Design of Group II Introns Yields Highly Active Ribozymes.Chembiochem : a European journal of chemical biology · 2025Article
- RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.Bioinformatics (Oxford, England) · 2024Article
- Deep generative design of RNA family sequences.Nature methods · 2024Article
- Computational design and experimental verification of pseudoknotted ribozymes.RNA (New York, N.Y.) · 2023Article
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- MoiRNAiFold: a novel tool for complex in silico RNA design.Nucleic acids research · 2021Article
- A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.International journal of molecular sciences · 2021Article
- Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes.Biochemistry · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- Solving the RNA design problem with reinforcement learning.PLoS computational biology · 2018Article
- RNA folding kinetics using Monte Carlo and Gillespie algorithms.Journal of mathematical biology · 2018Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- Biomedical Applications of RNA-Based Devices.Current opinion in biomedical engineering · 2017Article
- RNA inverse folding using Monte Carlo tree search.BMC bioinformatics · 2017Article
- RNAiFold2T: Constraint Programming design of thermo-IRES switches.Bioinformatics (Oxford, England) · 2016Article
- Multi-objective optimization for RNA design with multiple target secondary structures.BMC bioinformatics · 2015Article
- RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.Nucleic acids research · 2015Article
- Fast, approximate kinetics of RNA folding.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.
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