dc.contributor.author | Pan, Keyao | |
dc.contributor.author | Bricker, William P | |
dc.contributor.author | Ratanalert, Sakul | |
dc.contributor.author | Bathe, Mark | |
dc.date.accessioned | 2018-03-20T19:40:47Z | |
dc.date.available | 2018-03-20T19:40:47Z | |
dc.date.issued | 2017-06 | |
dc.date.submitted | 2017-04 | |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issn | 1362-4962 | |
dc.identifier.uri | http://hdl.handle.net/1721.1/114242 | |
dc.description.abstract | 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. | en_US |
dc.description.sponsorship | United States. Office of Naval Research (Grant N00014-12-1-0621) | en_US |
dc.description.sponsorship | United States. Army Research Office (Grant W911NF1210420) | en_US |
dc.description.sponsorship | National Science Foundation (U.S.) (Grant 1560425) | en_US |
dc.description.sponsorship | United States. Office of Naval Research (Grant N00014-13-1-0664) | en_US |
dc.description.sponsorship | United States. Office of Naval Research (Grant N00014-15-1-2830) | en_US |
dc.publisher | Oxford University Press | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1093/NAR/GKX378 | en_US |
dc.rights | Creative Commons Attribution 4.0 International License | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | en_US |
dc.source | Nucleic Acids Research | en_US |
dc.title | Structure and conformational dynamics of scaffolded DNA origami nanoparticles | en_US |
dc.type | Article | en_US |
dc.identifier.citation | 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 | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Biological Engineering | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Chemical Engineering | en_US |
dc.contributor.mitauthor | Pan, Keyao | |
dc.contributor.mitauthor | Bricker, William P | |
dc.contributor.mitauthor | Ratanalert, Sakul | |
dc.contributor.mitauthor | Bathe, Mark | |
dc.relation.journal | Nucleic Acids Research | en_US |
dc.eprint.version | Final published version | en_US |
dc.type.uri | http://purl.org/eprint/type/JournalArticle | en_US |
eprint.status | http://purl.org/eprint/status/PeerReviewed | en_US |
dc.date.updated | 2018-02-23T20:15:43Z | |
dspace.orderedauthors | Pan, Keyao; Bricker, William P.; Ratanalert, Sakul; Bathe, Mark | en_US |
dspace.embargo.terms | N | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-4573-5206 | |
dc.identifier.orcid | https://orcid.org/0000-0002-1766-807X | |
dc.identifier.orcid | https://orcid.org/0000-0002-6199-6855 | |
mit.license | PUBLISHER_CC | en_US |