Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures o...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2014
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| Online Access: | http://hdl.handle.net/1721.1/92017 https://orcid.org/0000-0002-9538-4996 https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-6199-6855 |
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| author | Pan, Keyao Kim, Do-Nyun Zhang, Fei Yan, Hao Bathe, Mark Adendorff, Matthew Ralph |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Pan, Keyao Kim, Do-Nyun Zhang, Fei Yan, Hao Bathe, Mark Adendorff, Matthew Ralph |
| author_sort | Pan, Keyao |
| collection | MIT |
| description | DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. |
| first_indexed | 2024-09-23T11:13:06Z |
| format | Article |
| id | mit-1721.1/92017 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:13:06Z |
| publishDate | 2014 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/920172022-09-27T17:56:22Z Lattice-free prediction of three-dimensional structure of programmed DNA assemblies Pan, Keyao Kim, Do-Nyun Zhang, Fei Yan, Hao Bathe, Mark Adendorff, Matthew Ralph Massachusetts Institute of Technology. Department of Biological Engineering Pan, Keyao Adendorff, Matthew Ralph Bathe, Mark DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. United States. Office of Naval Research (ONR N000141210621) National Science Foundation (U.S.) (NSF-DMREF Program CMMI1334109) 2014-12-03T17:00:55Z 2014-12-03T17:00:55Z 2014-12 2014-07 Article http://purl.org/eprint/type/JournalArticle 2041-1723 http://hdl.handle.net/1721.1/92017 Pan, Keyao et al. “Lattice-Free Prediction of Three-Dimensional Structure of Programmed DNA Assemblies.” Nature Communications 5 (2014): 5578. https://orcid.org/0000-0002-9538-4996 https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-6199-6855 en_US http://dx.doi.org/10.1038/ncomms6578 Nature Communications Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Nature |
| spellingShingle | Pan, Keyao Kim, Do-Nyun Zhang, Fei Yan, Hao Bathe, Mark Adendorff, Matthew Ralph Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title | Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title_full | Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title_fullStr | Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title_full_unstemmed | Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title_short | Lattice-free prediction of three-dimensional structure of programmed DNA assemblies |
| title_sort | lattice free prediction of three dimensional structure of programmed dna assemblies |
| url | http://hdl.handle.net/1721.1/92017 https://orcid.org/0000-0002-9538-4996 https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-6199-6855 |
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