Complex wireframe DNA origami nanostructures with multi-arm junction vertices

Journal name:
Nature Nanotechnology
Volume:
10,
Pages:
779–784
Year published:
DOI:
doi:10.1038/nnano.2015.162
Received
Accepted
Published online

Structural DNA nanotechnology1, 2, 3, 4 and the DNA origami technique5, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures6, 7, 8, 9, 10. These structures are, however, typically formed of tightly packed parallel helices5, 6, 7, 8, 9. The development of wireframe structures10, 11 should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2–10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles12 of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.

At a glance

Figures

  1. Design principles.
    Figure 1: Design principles.

    a, Left: an arbitrary wireframe pattern composed of line segments (grey) and vertices (blue). Right: steps to route a scaffold. First, double all the line segments from the original pattern. Second, connect the lines that meet at each vertex. Third, ‘loop’ and ‘bridge’ all the lines into one continuous scaffold. b, A DNA helical model of a 4 × 4 junction (top) and a line model of the 4 × 4 junction (bottom). Each vertex is designed as an n × 4 junction. The angle of adjacent arms in one junction can be adjusted by inserting poly T loops (red dots) and leaving unpaired nucleotides in the scaffold strand opposite to the poly T loop (pink dots). c, Adding staple strands on two different types of edge (five-turn long edges are used here for illustration): the edge with two antiparallel scaffolds (top) and the edge with a scaffold bridge (Holliday junction) in the middle (bottom). Arrows indicate the direction from the 5′ end to the 3′ end of the DNA. In b and c, dark blue strands represent the scaffold strand and grey and cyan strands are the staple strands.

  2. Scaffold folding paths and representative AFM images for the simple Platonic tiling.
    Figure 2: Scaffold folding paths and representative AFM images for the simple Platonic tiling.

    ac, Platonic tiling based on hexagon, square and triangle geometries, respectively. d, A 7 × 8 square Platonic tiling composed of two scaffolds (the black-blue loop on the left is a PhiX174 scaffold, and the coloured loop on the right is an M13mp18 scaffold). e, A lattice with 17 × 19 square cavities. All scale bars, 100 nm.

  3. Scaffold folding path and representative AFM images for intricate 2D patterns.
    Figure 3: Scaffold folding path and representative AFM images for intricate 2D patterns.

    a, A star-shaped pattern without translational symmetry. b, A Penrose tiling. c, An eight-fold quasi-crystalline pattern. df, Three curved structures: a wavy grid (d), a sphere array (e) and a fishnet (f). g, Flower-and-bird pattern. All scale bars, 100 nm. Two scaffolds (one colourful and one black-blue) are used in c and g.

  4. 3D wireframe Archimedean solid structures.
    Figure 4: 3D wireframe Archimedean solid structures.

    a, A 3D model of an Archimedean solid cuboctahedron with 12 vertices and 24 edges. Each vertex is a 4 × 4 junction and each edge is a 14-turn-long double DNA duplex. b, Left: models showing possible conformations of the structure when deposited on a mica surface. Right: corresponding AFM images. c, Reconfiguration between three and two dimensions can be realized by strand displacement by adding fuel and set strands. Top: reconfiguration schematics. Bottom: AFM images showing the transition. All scale bars in AFM images, 100 nm. d, 3D model of a snub cube with 24 vertices and 60 edges. Each vertex is a 5 × 4 junction and each edge is a five-turn double DNA duplex. e, Three views of the DNA snub cube from the design model (top) and density maps reconstructed from cryo-EM images (bottom) along the two-, three- and four-fold rotational symmetry axes, respectively.

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Author information

Affiliations

  1. Center for Molecular Design and Biomimetics, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA

    • Fei Zhang,
    • Shuoxing Jiang,
    • Yan Liu &
    • Hao Yan
  2. Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA

    • Siyu Wu,
    • Yulin Li &
    • Chengde Mao

Contributions

H.Y., Y.L. and F.Z. conceived and designed the experiment. F.Z., S.J., S.W. and Y.L. performed the experiments. F.Z., S.J., S.W. and Y.L. analysed the data. All authors discussed the results. All authors contributed to the writing the manuscript.

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The authors declare no competing financial interests.

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