Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
<jats:title>Abstract</jats:title> <jats:p>Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-heli...
| Main Authors: | , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press (OUP)
2023
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| Online Access: | https://hdl.handle.net/1721.1/147752 |
| _version_ | 1826215979264245760 |
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| author | Jun, Hyungmin Wang, Xiao Parsons, Molly F Bricker, William P John, Torsten Li, Shanshan Jackson, Steve Chiu, Wah Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Jun, Hyungmin Wang, Xiao Parsons, Molly F Bricker, William P John, Torsten Li, Shanshan Jackson, Steve Chiu, Wah Bathe, Mark |
| author_sort | Jun, Hyungmin |
| collection | MIT |
| description | <jats:title>Abstract</jats:title>
<jats:p>Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.</jats:p> |
| first_indexed | 2024-09-23T16:40:26Z |
| format | Article |
| id | mit-1721.1/147752 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T16:40:26Z |
| publishDate | 2023 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | mit-1721.1/1477522023-01-27T03:02:11Z Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami Jun, Hyungmin Wang, Xiao Parsons, Molly F Bricker, William P John, Torsten Li, Shanshan Jackson, Steve Chiu, Wah Bathe, Mark Massachusetts Institute of Technology. Department of Biological Engineering <jats:title>Abstract</jats:title> <jats:p>Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.</jats:p> 2023-01-26T18:49:55Z 2023-01-26T18:49:55Z 2021 2023-01-26T18:47:16Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/147752 Jun, Hyungmin, Wang, Xiao, Parsons, Molly F, Bricker, William P, John, Torsten et al. 2021. "Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami." Nucleic Acids Research, 49 (18). en 10.1093/NAR/GKAB762 Nucleic Acids Research Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Oxford University Press (OUP) Nucleic Acids Research |
| spellingShingle | Jun, Hyungmin Wang, Xiao Parsons, Molly F Bricker, William P John, Torsten Li, Shanshan Jackson, Steve Chiu, Wah Bathe, Mark Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title | Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title_full | Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title_fullStr | Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title_full_unstemmed | Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title_short | Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami |
| title_sort | rapid prototyping of arbitrary 2d and 3d wireframe dna origami |
| url | https://hdl.handle.net/1721.1/147752 |
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