Mechanism of DNA origami folding elucidated by mesoscopic simulations

Marcello DeLuca, Daniel Duke, Tao Ye, Michael Poirier, Yonggang Ke, Carlos Castro and Gaurav Arya ()
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Marcello DeLuca: Duke University
Daniel Duke: Duke University
Tao Ye: University of California
Michael Poirier: The Ohio State University
Yonggang Ke: Georgia Institute of Technology and Emory University
Carlos Castro: The Ohio State University
Gaurav Arya: Duke University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46998-y

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