Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures Article Swipe
Rupam Saha
,
Daichi Hayakawa
,
Thomas E. Videbæk
,
M.L. PRICE
,
Wei-Shao Wei
,
Juanita Pombo
,
Daniel Linden Duke
,
Gaurav Arya
,
Gregory M. Grason
,
W. Benjamin Rogers
,
Seth Fraden
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2502.05388
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2502.05388
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.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- http://arxiv.org/abs/2502.05388
- https://arxiv.org/pdf/2502.05388
- OA Status
- green
- Cited By
- 1
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4407384803Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2502.05388Digital Object Identifier
- Title
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Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructuresWork title
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preprintOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-02-08Full publication date if available
- Authors
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Rupam Saha, Daichi Hayakawa, Thomas E. Videbæk, M.L. PRICE, Wei-Shao Wei, Juanita Pombo, Daniel Linden Duke, Gaurav Arya, Gregory M. Grason, W. Benjamin Rogers, Seth FradenList of authors in order
- Landing page
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https://arxiv.org/abs/2502.05388Publisher landing page
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https://arxiv.org/pdf/2502.05388Direct link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://arxiv.org/pdf/2502.05388Direct OA link when available
- Concepts
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DNA origami, Modular design, Computer science, Nanostructure, Nanotechnology, DNA, DNA nanotechnology, Engineering drawing, Engineering, Materials science, Chemistry, Programming language, BiochemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1Per-year citation counts (last 5 years)
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.strategy | 122 |
| abstract_inverted_index.validate | 86 |
| abstract_inverted_index.conserves | 32 |
| abstract_inverted_index.cryogenic | 75 |
| abstract_inverted_index.different | 37 |
| abstract_inverted_index.efficient | 132 |
| abstract_inverted_index.including | 18, 105 |
| abstract_inverted_index.molecular | 82 |
| abstract_inverted_index.nanoscale | 16 |
| abstract_inverted_index.preserves | 40 |
| abstract_inverted_index.promising | 130 |
| abstract_inverted_index.providing | 128 |
| abstract_inverted_index.structure | 29 |
| abstract_inverted_index.synthetic | 136 |
| abstract_inverted_index.adjustable | 69 |
| abstract_inverted_index.assembling | 13, 99 |
| abstract_inverted_index.challenges | 11 |
| abstract_inverted_index.completely | 31 |
| abstract_inverted_index.controlled | 109 |
| abstract_inverted_index.curvature, | 113 |
| abstract_inverted_index.curvature. | 23, 120 |
| abstract_inverted_index.nonuniform | 21 |
| abstract_inverted_index.sequences. | 73 |
| abstract_inverted_index.versatile, | 127 |
| abstract_inverted_index.anisotropic | 106 |
| abstract_inverted_index.demonstrate | 94 |
| abstract_inverted_index.fabrication | 137 |
| abstract_inverted_index.independent | 60 |
| abstract_inverted_index.microscopy, | 77 |
| abstract_inverted_index.programming | 61 |
| abstract_inverted_index.structures, | 17, 104 |
| abstract_inverted_index.dramatically | 50 |
| abstract_inverted_index.interactions | 64, 111 |
| abstract_inverted_index.simulations, | 84 |
| abstract_inverted_index.geometrically | 14 |
| abstract_inverted_index.inter-subunit | 110 |
| abstract_inverted_index.self-limiting | 103 |
| abstract_inverted_index.coarse-grained | 81 |
| abstract_inverted_index.cost-effective | 125 |
| abstract_inverted_index.nanostructures. | 140 |
| abstract_inverted_index.electrophoresis, | 79 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 11 |
| citation_normalized_percentile |