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

Keyao Pan, Do-Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan and Mark Bathe ()
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Keyao Pan: Massachusetts Institute of Technology
Do-Nyun Kim: Seoul National University
Fei Zhang: Center for Molecular Design and Biomimicry, the Biodesign Institute, Arizona State University
Matthew R. Adendorff: Massachusetts Institute of Technology
Hao Yan: Center for Molecular Design and Biomimicry, the Biodesign Institute, Arizona State University
Mark Bathe: Massachusetts Institute of Technology

Nature Communications, 2014, vol. 5, issue 1, 1-7

Abstract: Abstract 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.

Date: 2014
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DOI: 10.1038/ncomms6578

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