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

Keyao Pan, Do Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan, Mark Bathe

Research output: Contribution to journalArticle

55 Citations (Scopus)

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 languageEnglish
Article number5578
JournalNature Communications
Volume5
DOIs
Publication statusPublished - 2014

Fingerprint

assemblies
deoxyribonucleic acid
Molecular Weight
DNA
predictions
Nucleic Acids
molecular weight
Molecular weight
tiles
nucleic acids
Materials science
materials science
Tile
ribbons
topology
Topology
Crystalline materials
rings
Experiments

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 journalArticle

Pan, Keyao ; Kim, Do Nyun ; Zhang, Fei ; Adendorff, Matthew R. ; Yan, Hao ; Bathe, Mark. / Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. In: Nature Communications. 2014 ; Vol. 5.
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