Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures
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| Main Authors: | , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866929703684669440 |
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| author | Saha, Rupam Hayakawa, Daichi Videbaek, Thomas E. Price, Mason Wei, Wei-Shao Pombo, Juanita Duke, Daniel Arya, Gaurav Grason, Gregory M. Rogers, W. Benjamin Fraden, Seth |
| author_facet | Saha, Rupam Hayakawa, Daichi Videbaek, Thomas E. Price, Mason Wei, Wei-Shao Pombo, Juanita Duke, Daniel Arya, Gaurav Grason, Gregory M. Rogers, W. Benjamin Fraden, Seth |
| contents | We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. 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 molecular dynamics simulations, we validate a set of robust design rules. We demonstrate the method's utility by assembling a variety of self-limiting structures, including anisotropic shells with controlled inter-subunit interactions and curvature, and a toroid with globally varying curvature. Our strategy is both cost-effective and versatile, providing a promising and efficient solution for the synthetic fabrication of complex nanostructures. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2502_05388 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures Saha, Rupam Hayakawa, Daichi Videbaek, Thomas E. Price, Mason Wei, Wei-Shao Pombo, Juanita Duke, Daniel Arya, Gaurav Grason, Gregory M. Rogers, W. Benjamin Fraden, Seth Soft Condensed Matter We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. 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 molecular dynamics simulations, we validate a set of robust design rules. We demonstrate the method's utility by assembling a variety of self-limiting structures, including anisotropic shells with controlled inter-subunit interactions and curvature, and a toroid with globally varying curvature. Our strategy is both cost-effective and versatile, providing a promising and efficient solution for the synthetic fabrication of complex nanostructures. |
| title | Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2502.05388 |