TY - JOUR
T1 - Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
AU - Pan, Keyao
AU - Kim, Do Nyun
AU - Zhang, Fei
AU - Adendorff, Matthew R.
AU - Yan, Hao
AU - Bathe, Mark
N1 - Funding Information:
This research was funded by the Office of Naval Research (ONR N000141210621) to K.P. and M.B. and the National Science Foundation (NSF-DMREF program CMMI1334109) to K.P., M.R.A. and M.B. D-N.K. is supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (NRF 2013R1A1A1010626). H.Y. and F.Z. acknowledge funding from the National Science Foundation (NSF-DMREF program CMMI1334109) and the Presidential Strategic Initiative Fund from Arizona State University. The authors are grateful to Dongran Han for useful discussions.
PY - 2014/12
Y1 - 2014/12
N2 - 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.
AB - 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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U2 - 10.1038/ncomms6578
DO - 10.1038/ncomms6578
M3 - Article
C2 - 25470497
AN - SCOPUS:84922729623
VL - 5
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 5578
ER -