Structure and conformational dynamics of scaffolded DNA origami nanoparticles
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fu lly determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on th...
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| Format: | Article |
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Oxford University Press
2018
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| Online Access: | http://hdl.handle.net/1721.1/114242 https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 |
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| author | Pan, Keyao Bricker, William P Ratanalert, Sakul Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Pan, Keyao Bricker, William P Ratanalert, Sakul Bathe, Mark |
| author_sort | Pan, Keyao |
| collection | MIT |
| description | Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fu lly determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5- 100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarsegrained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DXbased DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural andmechanical properties of DXbased assemblies that are inaccessible to all-atom based models alone. |
| first_indexed | 2024-09-23T12:28:17Z |
| format | Article |
| id | mit-1721.1/114242 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T12:28:17Z |
| publishDate | 2018 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/1142422022-10-01T09:14:35Z Structure and conformational dynamics of scaffolded DNA origami nanoparticles Pan, Keyao Bricker, William P Ratanalert, Sakul Bathe, Mark Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Chemical Engineering Pan, Keyao Bricker, William P Ratanalert, Sakul Bathe, Mark Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fu lly determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5- 100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarsegrained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DXbased DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural andmechanical properties of DXbased assemblies that are inaccessible to all-atom based models alone. United States. Office of Naval Research (Grant N00014-12-1-0621) United States. Army Research Office (Grant W911NF1210420) National Science Foundation (U.S.) (Grant 1560425) United States. Office of Naval Research (Grant N00014-13-1-0664) United States. Office of Naval Research (Grant N00014-15-1-2830) 2018-03-20T19:40:47Z 2018-03-20T19:40:47Z 2017-06 2017-04 2018-02-23T20:15:43Z Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/114242 Pan, Keyao et al. “Structure and Conformational Dynamics of Scaffolded DNA Origami Nanoparticles.” Nucleic Acids Research 45, 11 (May 2017): 6284–6298 © 2017 The Authors https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 http://dx.doi.org/10.1093/NAR/GKX378 Nucleic Acids Research Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by-nc/4.0/ application/pdf Oxford University Press Nucleic Acids Research |
| spellingShingle | Pan, Keyao Bricker, William P Ratanalert, Sakul Bathe, Mark Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title_full | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title_fullStr | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title_full_unstemmed | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title_short | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| title_sort | structure and conformational dynamics of scaffolded dna origami nanoparticles |
| url | http://hdl.handle.net/1721.1/114242 https://orcid.org/0000-0003-4573-5206 https://orcid.org/0000-0002-1766-807X https://orcid.org/0000-0002-6199-6855 |
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