Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
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Bathe_Lattice-free prediction.pdf
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1.67 MB
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Adobe PDF
Checksum (MD5)
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Author(s)
Pan, Keyao
Kim, Do-Nyun
Zhang, Fei
Yan, Hao
Bathe, Mark
Adendorff, Matthew Ralph
Date Issued
December 2014
Journal
Nature Communications
Publisher
Nature Publishing Group
Citation
Pan, Keyao et al. “Lattice-Free Prediction of Three-Dimensional Structure of Programmed DNA Assemblies.” Nature Communications 5 (2014): 5578.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1038/ncomms6578
