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December 11, 2025Nature Communications4 citationsOpen Access

Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures

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RSRupam SahaDHDaichi HayakawaTVThomas E. Videbæk

Key Points

  • The aim is to develop a modular design for assembling complex DNA origami nanostructures.
  • Implemented a modular DNA origami design approach.
  • Used cryogenic electron microscopy and gel electrophoresis for validation.
  • Conducted coarse-grained simulations to assess design rules.
  • Demonstrated assembly of diverse self-limiting structures like anisotropic shells and an icosahedral shell.
  • Validated design rules leading to efficient nanostructure assembly.
  • Achieved cost reductions by conserving DNA staples between designs.

Abstract

Self-assembly of nanoscale building blocks with programmable geometries and interactions offers a powerful route to engineer materials that mimic the complexity of biological structures. DNA origami provides an exceptional platform for this purpose, enabling precise control over subunit shape, binding angles, and interaction specificity. Here we present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform curvatures. This approach features a core structure that completely conserves the scaffold routing across different designs and preserves more than 70% of the DNA staples between designs, dramatically reducing both cost and effort, while enabling precise and independent programming of subunit interactions and binding angles through adjustable overhang lengths and sequences. Using cryogenic electron microscopy, gel electrophoresis, and coarse-grained simulations, we validate a set of robust design rules and demonstrate the assembly of diverse self-limiting structures, including anisotropic shells, a T = 13 icosahedral shell, and a toroid with globally varying curvature. This modular strategy provides an efficient and cost-effective framework for the synthetic fabrication of complex nanostructures.

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Cite This Study

Saha et al. (2025) studied this question.

synapsesocial.com/papers/69401b172d562116f28f7340https://doi.org/10.1038/s41467-025-66195-9
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