TY - JOUR
T1 - Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles
AU - Matthies, Michael
AU - Agarwal, Nayan P.
AU - Poppleton, Erik
AU - Joshi, Foram M.
AU - Šulc, Petr
AU - Schmidt, Thorsten L.
N1 - Funding Information:
We acknowledge the use of the imaging facilities in the Dresden Center for Nanoanalysis(DCN) and skillful advice from Dr. Markus Löffler as well as access to the AFM of Prof. Michael Mertig. We also acknowledge Anne Schulze for her administrative assistance. This work was funded by the DFG through the Center for Advancing Electronics Dresden (cfaed). Part of the simulations work used the Extreme Science and Engineering Discovery Environment (XSEDE),71 which is supported by National Science Foundation grant number ACI-154856 through allocation MCB180033. P.Š. further acknowledges the donation of GPU cards from the NVIDIA Corporation.
Publisher Copyright:
© 2019 American Chemical Society.
PY - 2019/2/26
Y1 - 2019/2/26
N2 - The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.
AB - The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.
KW - Molecular dynamics simulations
KW - Single-stranded tiles
KW - Structural DNA nanotechnology
KW - Triangulated wireframe structures
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U2 - 10.1021/acsnano.8b08009
DO - 10.1021/acsnano.8b08009
M3 - Article
C2 - 30624898
AN - SCOPUS:85060389225
SN - 1936-0851
VL - 13
SP - 1839
EP - 1848
JO - ACS nano
JF - ACS nano
IS - 2
ER -