ArticleNature communications2024
Mechanism of DNA origami folding elucidated by mesoscopic simulations.
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 12 papers.
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Who cites it
12 citing papers in PubMed.
- A nanoscale Jitterbug transformer from DNA.Nature communications · 2026Article
- Optimising DNA origami assembly by reducing off-target interactions.Nature communications · 2026Article
- DNA Origami and Their Application in Biosensors.Biosensors · 2026Review
- Mesophases as stepping stones to enhance crystallization kinetics in nanoparticle self-assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Complex cooperativity in DNA origami revealed via design-dependent defectivity.Nucleic acids research · 2026Article
- Unraveling the Folding Dynamics of DNA Origami Structures.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Programmable DNA aptamer logic gates: from structural design to integrated systems for intelligent nanoscale biosensors.Analytical and bioanalytical chemistry · 2025Review
- How We Simulate DNA Origami.Small methods · 2025Article
- Folding Competition and Dynamic Transformation in DNA Origami: Parallel Versus Antiparallel Crossovers.Small methods · 2025Article
- Article
- Counterions influence the isothermal self-assembly of DNA nanostructures.Science advances · 2025Article
- Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells.Discover nano · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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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.