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...
| Main Authors: | , , , |
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| Other Authors: | |
| 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 |
| Summary: | 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. |
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