Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
| Autor: | Hao Yan, Mark Bathe, Do-Nyun Kim, Keyao Pan, Matthew R. Adendorff, Fei Zhang |
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| Přispěvatelé: | Massachusetts Institute of Technology. Department of Biological Engineering, Pan, Keyao, Adendorff, Matthew Ralph, Bathe, Mark |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Models
Molecular Materials science General Physics and Astronomy 02 engineering and technology Bioinformatics General Biochemistry Genetics and Molecular Biology Article 03 medical and health sciences chemistry.chemical_compound Planar Lattice (order) Tensegrity Ribbon Nanotechnology Protein secondary structure 030304 developmental biology 0303 health sciences Multidisciplinary Sequence design General Chemistry DNA 021001 nanoscience & nanotechnology chemistry Nucleic Acid Conformation 0210 nano-technology Biological system |
| Zdroj: | Nature Nature Communications |
| Popis: | 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) |
| Databáze: | OpenAIRE |
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