ArticleNano letters2016
Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.
Article in Nano letters, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 61 citations in OpenAlex.
- Reconfigurable Nucleic Acid Nanoparticles with Therapeutic RNAi Responses to Intracellular Disease Markers.Advanced functional materials · 2025Article
- Nucleic acid nanobiosystems for cancer theranostics: an overview of emerging trends and challenges.Nanomedicine (London, England) · 2025Review
- Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells.ACS nano · 2025Review
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles.ACS applied materials & interfaces · 2023Article
- Dynamic Nanostructures for Conditional Activation and Deactivation of Biological Pathways.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2022Article
- VfoldMCPX: predicting multistrand RNA complexes.RNA (New York, N.Y.) · 2022Article
- Programmable siRNA pro-drugs that activate RNAi activity in response to specific cellular RNA biomarkers.Molecular therapy. Nucleic acids · 2022Article
- Exosomes as natural delivery carriers for programmable therapeutic nucleic acid nanoparticles (NANPs).Advanced drug delivery reviews · 2021Review
- Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities.ACS applied materials & interfaces · 2021Article
- A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.International journal of molecular sciences · 2021Article
- Review
- Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles.Nature protocols · 2020Article
- Innate immune responses triggered by nucleic acids inspire the design of immunomodulatory nucleic acid nanoparticles (NANPs).Current opinion in biotechnology · 2020Review
- Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties.Nanomedicine (London, England) · 2020Article
- Improved Nucleic Acid Therapy with Advanced Nanoscale Biotechnology.Molecular therapy. Nucleic acids · 2020Review
- Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies.Molecules (Basel, Switzerland) · 2019Review
- Modulating Immune Response with Nucleic Acid Nanoparticles.Molecules (Basel, Switzerland) · 2019Review
- Numerical operations in living cells by programmable RNA devices.Science advances · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
RNA is an attractive material for the creation of molecular logic gates that release programmed functionalities only in the presence of specific molecular interaction partners. Here we present HyperFold, a multistrand RNA/DNA structure prediction approach for predicting nucleic acid complexes that can contain pseudoknots. We show that HyperFold also performs competitively compared to other published folding algorithms. We performed a large variety of RNA/DNA hybrid reassociation experiments for different concentrations, DNA toehold lengths, and G+C content and find that the observed tendencies for reassociation correspond well to computational predictions. Importantly, we apply this method to the design and experimental verification of a two-stranded RNA molecular switch that upon binding to a single-stranded RNA toehold disease-marker trigger mRNA changes its conformation releasing an shRNA-like Dicer substrate structure. To demonstrate the concept, connective tissue growth factor (CTGF) mRNA and enhanced green fluorescent protein (eGFP) mRNA were chosen as trigger and target sequences, respectively. In vitro experiments confirm the formation of an RNA switch and demonstrate that the functional unit is being released when the trigger RNA interacts with the switch toehold. The designed RNA switch is shown to be functional in MDA-MB-231 breast cancer cells. Several other switches were also designed and tested. We conclude that this approach has considerable potential because, in principle, it allows the release of an siRNA designed against a gene that differs from the gene that is utilized as a biomarker for a disease state.
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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.