ArticleMethods (San Diego, Calif.)2014
Computational and experimental characterization of RNA cubic nanoscaffolds.
Article in Methods (San Diego, Calif.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Biological Nanoscaffolds from Hierarchical Construction to Applications.Molecules (Basel, Switzerland) · 2026Review
- Expanding Chemical Space of Nucleic Acid Nanoparticles for Tunable Antiviral-Like Immunomodulatory Responses and Potent Adjuvant Activity.Advanced functional materials · 2026Article
- Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles.ACS nano · 2025Article
- Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications.Biochemistry · 2024Article
- Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction.PloS one · 2024Article
- Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs)Bioconjugate chemistry · 2023Article
- 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
- Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts.Frontiers in bioengineering and biotechnology · 2023Review
- Light-Assisted Drying for the Thermal Stabilization of Nucleic Acid Nanoparticles and Other Biologics.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Dissecting Functional Biological Interactions Using Modular RNA Nanoparticles.Molecules (Basel, Switzerland) · 2022Review
- 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
- Expanding Structural Space for Immunomodulatory Nucleic Acid Nanoparticles (Nanps) via Spatial Arrangement of Their Therapeutic Moieties.Advanced functional materials · 2022Article
- The Application of Light-Assisted Drying to the Thermal Stabilization of Nucleic Acid Nanoparticles.Biopreservation and biobanking · 2022Article
- Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures.Small (Weinheim an der Bergstrasse, Germany) · 2022Article
- Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes.RNA (New York, N.Y.) · 2021Article
- Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects.Advanced drug delivery reviews · 2021Review
- Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance In Vitro.ACS applied materials & interfaces · 2020Article
- A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (Nanps) for controlled gene silencing, immunostimulation, and biodistribution.Nanomedicine : nanotechnology, biology, and medicine · 2020Article
- Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies.Molecules (Basel, Switzerland) · 2019Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles.
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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.