Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists
Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto ‘raw se...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023002490 |
| _version_ | 1827577578768039936 |
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| author | Ben Shirt-Ediss Jordan Connolly Juan Elezgaray Emanuela Torelli Silvia Adriana Navarro Jaume Bacardit Natalio Krasnogor |
| author_facet | Ben Shirt-Ediss Jordan Connolly Juan Elezgaray Emanuela Torelli Silvia Adriana Navarro Jaume Bacardit Natalio Krasnogor |
| author_sort | Ben Shirt-Ediss |
| collection | DOAJ |
| description | Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto ‘raw sequence’ exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a ‘guide schematic’ resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io. |
| first_indexed | 2024-03-08T21:29:49Z |
| format | Article |
| id | doaj.art-0f8df21e9fbf40bc899725906c767fe8 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:29:49Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-0f8df21e9fbf40bc899725906c767fe82023-12-21T07:31:48ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012136153626Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence listsBen Shirt-Ediss0Jordan Connolly1Juan Elezgaray2Emanuela Torelli3Silvia Adriana Navarro4Jaume Bacardit5Natalio Krasnogor6Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UKInterdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UKCentre de Recherche Paul Pascal, CNRS, UMR503, Pessac 33600, FranceInterdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UKInterdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UKInterdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UKInterdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK; Corresponding author.Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto ‘raw sequence’ exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a ‘guide schematic’ resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.http://www.sciencedirect.com/science/article/pii/S2001037023002490DNA origamiDNA nanotechnologyReverse engineeringContact mapConstraint programmingSpring embedder |
| spellingShingle | Ben Shirt-Ediss Jordan Connolly Juan Elezgaray Emanuela Torelli Silvia Adriana Navarro Jaume Bacardit Natalio Krasnogor Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists Computational and Structural Biotechnology Journal DNA origami DNA nanotechnology Reverse engineering Contact map Constraint programming Spring embedder |
| title | Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists |
| title_full | Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists |
| title_fullStr | Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists |
| title_full_unstemmed | Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists |
| title_short | Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists |
| title_sort | reverse engineering dna origami nanostructure designs from raw scaffold and staple sequence lists |
| topic | DNA origami DNA nanotechnology Reverse engineering Contact map Constraint programming Spring embedder |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023002490 |
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