Autonomously designed free-form 2D DNA origami
Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands ne...
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| Format: | Article |
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American Association for the Advancement of Science (AAAS)
2019
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| Online Access: | http://hdl.handle.net/1721.1/120776 https://orcid.org/0000-0002-7108-1288 https://orcid.org/0000-0001-7122-1917 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 |
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| author | Zhang, Fei Qi, Xiaodong Yan, Hao Jun, Hyungmin Shepherd, Tyson R Ratanalert, Sakul Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Zhang, Fei Qi, Xiaodong Yan, Hao Jun, Hyungmin Shepherd, Tyson R Ratanalert, Sakul Bathe, Mark |
| author_sort | Zhang, Fei |
| collection | MIT |
| description | Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology. |
| first_indexed | 2024-09-23T10:37:56Z |
| format | Article |
| id | mit-1721.1/120776 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T10:37:56Z |
| publishDate | 2019 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | dspace |
| spelling | mit-1721.1/1207762022-09-30T21:56:26Z Autonomously designed free-form 2D DNA origami Zhang, Fei Qi, Xiaodong Yan, Hao Jun, Hyungmin Shepherd, Tyson R Ratanalert, Sakul Bathe, Mark Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Chemical Engineering Jun, Hyungmin Shepherd, Tyson R Ratanalert, Sakul Bathe, Mark Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology. National Science Foundation (U.S.) (Grant CCF-1564025) National Science Foundation (U.S.) (Grant CMMI-1334109) Office of Naval Research (Grant N000141210621) 2019-03-07T14:12:07Z 2019-03-07T14:12:07Z 2018-11 2018-08 2019-02-15T14:29:20Z Article http://purl.org/eprint/type/JournalArticle 2375-2548 http://hdl.handle.net/1721.1/120776 Jun, Hyungmin et al. “Autonomously Designed Free-Form 2D DNA Origami.” Science Advances 5, 1 (January 2019): eaav0655 © 2019 The Authors https://orcid.org/0000-0002-7108-1288 https://orcid.org/0000-0001-7122-1917 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 http://dx.doi.org/10.1126/sciadv.aav0655 Science Advances Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/ application/pdf American Association for the Advancement of Science (AAAS) Science Advances |
| spellingShingle | Zhang, Fei Qi, Xiaodong Yan, Hao Jun, Hyungmin Shepherd, Tyson R Ratanalert, Sakul Bathe, Mark Autonomously designed free-form 2D DNA origami |
| title | Autonomously designed free-form 2D DNA origami |
| title_full | Autonomously designed free-form 2D DNA origami |
| title_fullStr | Autonomously designed free-form 2D DNA origami |
| title_full_unstemmed | Autonomously designed free-form 2D DNA origami |
| title_short | Autonomously designed free-form 2D DNA origami |
| title_sort | autonomously designed free form 2d dna origami |
| url | http://hdl.handle.net/1721.1/120776 https://orcid.org/0000-0002-7108-1288 https://orcid.org/0000-0001-7122-1917 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 |
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