ArticleACS nano2011
Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.
Article in ACS nano, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Self-Assembling RNA Nanostructures are Highly Sensitive to Environmental Conditions.Journal of molecular biology · 2026Article
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.Briefings in bioinformatics · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions.Molecules (Basel, Switzerland) · 2020Review
- Tuning the size, shape and structure of RNA nanoparticles for favorable cancer targeting and immunostimulation.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology · 2020Review
- Modulating Immune Response with Nucleic Acid Nanoparticles.Molecules (Basel, Switzerland) · 2019Review
- RCPred: RNA complex prediction as a constrained maximum weight clique problem.BMC bioinformatics · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- Accelerated RNA secondary structure design using preselected sequences for helices and loops.RNA (New York, N.Y.) · 2018Article
- Methods for construction and characterization of simple or special multifunctional RNA nanoparticles based on the 3WJ of phi29 DNA packaging motor.Methods (San Diego, Calif.) · 2018Review
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications.Wiley interdisciplinary reviews. RNA · 2018Review
- Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology.Nanomedicine : nanotechnology, biology, and medicine · 2017Article
- Advancement of the Emerging Field of RNA Nanotechnology.ACS nano · 2017Review
- Computational Generation of RNA Nanorings.Methods in molecular biology (Clifton, N.J.) · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We are presenting NanoFolder, a method for the prediction of the base pairing of potentially pseudoknotted multistrand RNA nanostructures. We show that the method outperforms several other structure prediction methods when applied to RNA complexes with non-nested base pairs. We extended this secondary structure prediction capability to allow RNA sequence design. Using native PAGE, we experimentally confirm that four in silico designed RNA strands corresponding to a triangular RNA structure form the expected stable complex.
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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.