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Mechanism of DNA origami folding elucidated by mesoscopic simulations.

Publication ,  Journal Article
DeLuca, M; Duke, D; Ye, T; Poirier, M; Ke, Y; Castro, C; Arya, G
Published in: Nature communications
April 2024

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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Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

April 2024

Volume

15

Issue

1

Start / End Page

3015

Related Subject Headings

  • Nucleic Acid Conformation
  • Nanotechnology
  • Nanostructures
  • Kinetics
  • DNA
 

Citation

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DeLuca, M., Duke, D., Ye, T., Poirier, M., Ke, Y., Castro, C., & Arya, G. (2024). Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nature Communications, 15(1), 3015. https://doi.org/10.1038/s41467-024-46998-y
DeLuca, Marcello, Daniel Duke, Tao Ye, Michael Poirier, Yonggang Ke, Carlos Castro, and Gaurav Arya. “Mechanism of DNA origami folding elucidated by mesoscopic simulations.Nature Communications 15, no. 1 (April 2024): 3015. https://doi.org/10.1038/s41467-024-46998-y.
DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, et al. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nature communications. 2024 Apr;15(1):3015.
DeLuca, Marcello, et al. “Mechanism of DNA origami folding elucidated by mesoscopic simulations.Nature Communications, vol. 15, no. 1, Apr. 2024, p. 3015. Epmc, doi:10.1038/s41467-024-46998-y.
DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, Arya G. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nature communications. 2024 Apr;15(1):3015.

Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

April 2024

Volume

15

Issue

1

Start / End Page

3015

Related Subject Headings

  • Nucleic Acid Conformation
  • Nanotechnology
  • Nanostructures
  • Kinetics
  • DNA