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.
| Original language | English |
|---|---|
| Article number | 5578 |
| Journal | Nature Communications |
| Volume | 5 |
| DOIs | |
| Publication status | Published - 2014 |
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ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Chemistry(all)
- Physics and Astronomy(all)
Cite this
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. / Pan, Keyao; Kim, Do Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark.
In: Nature Communications, Vol. 5, 5578, 2014.Research output: Contribution to journal › Article
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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
PY - 2014
Y1 - 2014
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
VL - 5
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 5578
ER -