ArticleNature communications2024
Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
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Who cites it
5 citing papers in PubMed.
- Advances in DNA nanostructures for pathogenic microorganisms.Materials today. Bio · 2026Review
- De novo design of DNA origami with a generative diffusion model.Nature communications · 2026Article
- Left-Handed Helices in DNA Nanotechnology.JACS Au · 2026Review
- SNUPI: A Computational Framework for Rapid Mechanical Analysis of Structured DNA Assemblies.JACS Au · 2025Article
- Realizing mechanical frustration at the nanoscale using DNA origami.Nature communications · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.
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Registered trials
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