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Nat Commun. 2014 Dec 3;5:5578. doi: 10.1038/ncomms6578.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies.

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Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, Massachusetts 02139, USA.
Department of Mechanical and Aerospace Engineering, Seoul National University, 301-dong 1516-ho, Gwanak-ro 1, Gwanak-gu, Seoul 151-744, Republic of Korea.
1] Center for Molecular Design and Biomimicry, the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.


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.

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