Research ArticleAPPLIED SCIENCES AND ENGINEERING

Autonomously designed free-form 2D DNA origami

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Science Advances  02 Jan 2019:
Vol. 5, no. 1, eaav0655
DOI: 10.1126/sciadv.aav0655
  • Fig. 1 Automated design of 2D wireframe scaffolded DNA origami objects.

    (A) Arbitrary target geometries can be specified in two ways: free-form boundary design (top), defining only the border of the target object, with the internal mesh geometry designed automatically, or free-form boundary and internal design (bottom), specifying the complete internal and external boundary geometry using piecewise continuous lines. (B) 2D line-based geometric representations are used as input to the algorithm that performs automatic scaffold and staple routings, converting each edge into two parallel duplexes joined by antiparallel crossovers. The single-stranded scaffold is routed throughout the entire origami object, with staple strands ranging in length from 20 to 60 nucleotides (nt; mean length, 40 nt). The circular maps illustrate the connectivities of staples hybridized to the circular scaffold in the final, self-assembled object, where each terminal point of the connecting staple line is located at the middle of its corresponding double-stranded DNA (dsDNA) domain in the folded line. caDNAno input files are also generated by the algorithm for manual editing of staple sequences or the scaffold routing path. (C) Staple sequences generated by the algorithm are used with the input scaffold to synthesize the programmed 2D wireframe object using standard one-pot thermal annealing.

  • Fig. 2 Automatic scaffold routing and staple sequence design.

    (A) Step 1: Double-line segments representing two parallel B-form DNA duplexes are generated along the edges of the target wireframe geometry. Step 2: Endpoints are joined such that each duplex becomes part of a loop (blue) containing all possible scaffold double crossovers (red) between closed loops. Step 3: The dual graph of the loop-crossover structure is introduced by converting each loop into a node and each double crossover into an edge. Step 4: The spanning tree of the dual graph is computed and inverted to route the ssDNA scaffold throughout the entire origami object automatically (position of the scaffold nick is indicated by a solid red circle), which enables the assignment of complementary staple strands. Step 5: Last, a 3D atomic-level structural model is generated, assuming canonical B-form DNA duplexes. (B) Design using continuous edge length for asymmetric and irregular shapes. The target geometry can be modeled in two ways: Using a discrete edge length consisting of multiples of 10.5 bp rounded to the nearest nucleotide or a continuous edge length with no constraint on length. Continuous edge lengths enable the design of objects with arbitrary edge lengths, which require duplex extensions to fill gaps in vertices. Both edge types were experimentally tested by folding and visualizing with AFM (figs. S6 to S8). The highest folding yields occurred with continuous edge length particles with unpaired nucleotides at the vertices. Excess scaffold is apparent in the AFM images at the position of the scaffold nick indicated in the scaffold routing diagram in (A). Scale bars, 150 nm.

  • Fig. 3 Designing variable vertex numbers, edge lengths, and mesh patterns.

    (A to C) Variable vertex numbers consisting of four-, five-, or six-arm junctions (A), variable edge lengths of 42, 63, and 84 bp (B), and variable mesh patterns, including quadrilateral, constant direction triangular, and mixed-direction triangular meshes (C), can be used. A mechanical model of the curved arm geometry predicts flexibility using the (left) constant direction triangular mesh pattern, with increased in-plane mechanical stiffness introduced by the (right) mixed-direction triangular mesh pattern, demonstrating the importance of internal mesh geometry on overall in-plane flexibility (fig. S37). Scale bars, 20 nm (atomic structures) and 50 and 150 nm (zoom-in and zoom-out AFM images, respectively).

  • Fig. 4 Fully automatic sequence design of 15 diverse scaffolded origami wireframe objects.

    Target 2D wireframe objects and DNA-based atomic models of nanostructures are shown with (blue) triangular, (red) quadrilateral, and (yellow) N-polygonal meshes, where N is the number of sides of the discrete mesh element. Representative AFM images for a square lattice and honeycomb lattice with triangular cavities, a rhombic tiling and a quarter circle with quadrilateral cavities, and a Cairo pentagonal tiling and lotus with N-polygon cavities are shown. Scale bars, 20 nm (atomic structures) and 50 nm (AFM images).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/1/eaav0655/DC1

    Supplementary Materials and Methods

    Fig. S1. Target geometry specification using piecewise continuous lines.

    Fig. S2. Schematic illustrating key steps in the design algorithm PERDIX for a 2D plate composed of a triangular mesh.

    Fig. S3. Scaffold and staple crossovers.

    Fig. S4. Discrete versus continuous edge lengths for asymmetric and irregular shapes.

    Fig. S5. Spanning the gap with precise lengths of dsDNA at an unequal vertex.

    Fig. S6. AFM imaging of the DNA quarter circle wireframe lattice (Type I: discrete edges).

    Fig. S7. AFM imaging of the DNA quarter circle wireframe lattice (Type II: continuous edges with no unpaired scaffold).

    Fig. S8. AFM imaging of the DNA quarter circle wireframe lattice (Type III: continuous edges with unpaired scaffold nucleotides as needed).

    Fig. S9. Nine target geometries used as input to the algorithm.

    Fig. S10. Base pair models with the scaffold and staple double crossovers for nine diverse 2D wireframe lattice structures.

    Fig. S11. Spanning trees of the dual graphs of the loop-crossover structures generated by the algorithm.

    Fig. S12. Scaffold routing path of nine diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S13. Staple design path of nine diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S14. Cylindrical representations of nine diverse 2D wireframe lattice structures.

    Fig. S15. Atomic models of nine diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S16. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with variable vertex degree.

    Fig. S17. Three different atomic representations of scaffolded DNA origami 2D lattice structures of different scales.

    Fig. S18. Three different atomic representations of scaffolded DNA origami 2D lattice structures designed with different mesh patterns.

    Fig. S19. Exported scalable vector graphics (SVG) schematic of the DNA four-sided polygon.

    Fig. S20. Exported SVG schematic of the DNA five-sided polygon.

    Fig. S21. Exported SVG schematic of the DNA six-sided polygon.

    Fig. S22. Exported SVG schematic of the 42-bp edge-length DNA L-shape wireframe lattice.

    Fig. S23. Exported SVG schematic of the 63-bp edge-length DNA L-shape wireframe lattice.

    Fig. S24. Exported SVG schematic of the 84-bp edge-length DNA L-shape wireframe lattice.

    Fig. S25. Exported SVG schematic of the DNA curved-arm wireframe lattice (quadrilateral meshes).

    Fig. S26. Exported SVG schematic of the DNA curved-arm wireframe lattice (triangular meshes).

    Fig. S27. Exported SVG schematic of the DNA curved-arm wireframe lattice (mixed meshes).

    Fig. S28. AFM imaging of the DNA four-sided polygon wireframe lattice.

    Fig. S29. AFM imaging of the DNA five-sided polygon wireframe lattice.

    Fig. S30. AFM imaging of the DNA six-sided polygon wireframe lattice.

    Fig. S31. AFM imaging of the DNA 42-bp edge-length L-shape DNA wireframe lattice.

    Fig. S32. AFM imaging of the DNA 63-bp edge-length L-shape wireframe lattice.

    Fig. S33. AFM imaging of the DNA 84-bp edge-length L-shape DNA wireframe lattice.

    Fig. S34. AFM imaging of the DNA curved-arm wireframe lattice (quadrilateral meshes).

    Fig. S35. AFM imaging of the DNA curved-arm wireframe lattice (triangular meshes).

    Fig. S36. AFM imaging of the DNA curved-arm wireframe lattice (mixed meshes).

    Fig. S37. Truss-like finite element simulation.

    Fig. S38. Fifteen target geometries used as input to the algorithm.

    Fig. S39. Base pair models with the scaffold and staple double crossovers for 15 diverse 2D wireframe lattice structures.

    Fig. S40. Fifteen spanning trees of the dual graph of the loop-crossover structures generated by the algorithm.

    Fig. S41. Scaffold-routing path of 15 diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S42. Staple design path of 15 diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S43. Cylindrical representations of 15 diverse 2D wireframe lattice structures.

    Fig. S44. Atomic models of 15 diverse 2D wireframe lattice structures generated by the algorithm.

    Fig. S45. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with triangular meshes.

    Fig. S46. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with quadrilateral meshes.

    Fig. S47. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with N-polygonal meshes.

    Fig. S48. Exported SVG schematic of the square wireframe lattice.

    Fig. S49. Exported SVG schematic of the honeycomb wireframe lattice.

    Fig. S50. Exported SVG schematic of the DNA rhombic tiling lattice.

    Fig. S51. Exported SVG schematic of the DNA quarter circle wireframe lattice.

    Fig. S52. Exported SVG schematic of the DNA Cairo pentagonal tiling.

    Fig. S53. Exported SVG schematic of the DNA lotus wireframe lattice.

    Fig. S54. AFM imaging of the DNA square wireframe lattice.

    Fig. S55. AFM imaging of the DNA honeycomb wireframe lattice.

    Fig. S56. AFM imaging of the DNA rhombic tiling wireframe lattice.

    Fig. S57. AFM imaging of the DNA Cairo pentagonal tiling wireframe lattice.

    Fig. S58. AFM imaging of the DNA lotus wireframe lattice.

    Table S1. Required scaffold lengths for 24 rendered DNA lattice structures.

    Table S2. Output from of the automatic sequence design for DNA origami 2D wireframe structures.

    Table S3. Folding yields determined by counting well-folded particles from AFM imaging.

    Table S4. Staple sequence for 84-bp edge-length DNA four-sided polygon origami folding.

    Table S5. Staple sequence for 84-bp edge-length DNA five-sided polygon origami folding.

    Table S6. Staple sequence for 84-bp edge-length DNA six-sided polygon origami folding.

    Table S7. Staple sequence for 42-bp edge-length DNA L-shape origami folding.

    Table S8. Staple sequence for 63-bp edge-length DNA L-shape origami folding.

    Table S9. Staple sequence for 84-bp edge-length DNA L-shape origami folding.

    Table S10. Staple sequence for DNA curved-beam origami folding (quadrilateral mesh pattern).

    Table S11. Staple sequence for DNA curved-beam origami folding (triangular mesh pattern).

    Table S12. Staple sequence for DNA curved-beam origami folding (mixed mesh pattern).

    Table S13. Staple sequence for 42-bp edge-length DNA plate origami folding.

    Table S14. Staple sequence for 42-bp edge-length DNA honeycomb origami folding.

    Table S15. Staple sequence for 84-bp edge-length DNA rhombic tiling origami folding.

    Table S16. Staple sequence for DNA quarter circle origami folding.

    Table S17. Staple sequence for DNA Cairo pentagonal tiling origami folding.

    Table S18. Staple sequence for DNA lotus origami folding.

    Table S19. Sequences for the 7249-nt (#1), 5386-nt (#2), and 2267-nt (#3) length scaffolds used.

    Movie S1. PERDIX run.

    Movie S2. PERDIX boundary design.

    Movie S3. PERDIX boundary and internal design.

    Movie S4. Atomic models: Different meshes.

    Movie S5. Atomic models: N-arm.

    Movie S6. Atomic models: L-shape.

    Movie S7. Atomic models: Curved arm.

    Data file S1. PERDIX software package

    Data file S2. PERDIX software documentation

    References (4046)

  • Supplementary Materials

    The PDF file includes:

    • Supplementary Materials and Methods
    • Fig. S1. Target geometry specification using piecewise continuous lines.
    • Fig. S2. Schematic illustrating key steps in the design algorithm PERDIX for a 2D plate composed of a triangular mesh.
    • Fig. S3. Scaffold and staple crossovers.
    • Fig. S4. Discrete versus continuous edge lengths for asymmetric and irregular shapes.
    • Fig. S5. Spanning the gap with precise lengths of dsDNA at an unequal vertex.
    • Fig. S6. AFM imaging of the DNA quarter circle wireframe lattice (Type I: discrete edges).
    • Fig. S7. AFM imaging of the DNA quarter circle wireframe lattice (Type II: continuous edges with no unpaired scaffold).
    • Fig. S8. AFM imaging of the DNA quarter circle wireframe lattice (Type III: continuous edges with unpaired scaffold nucleotides as needed).
    • Fig. S9. Nine target geometries used as input to the algorithm.
    • Fig. S10. Base pair models with the scaffold and staple double crossovers for nine diverse 2D wireframe lattice structures.
    • Fig. S11. Spanning trees of the dual graphs of the loop-crossover structures generated by the algorithm.
    • Fig. S12. Scaffold routing path of nine diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S13. Staple design path of nine diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S14. Cylindrical representations of nine diverse 2D wireframe lattice structures.
    • Fig. S15. Atomic models of nine diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S16. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with variable vertex degree.
    • Fig. S17. Three different atomic representations of scaffolded DNA origami 2D lattice structures of different scales.
    • Fig. S18. Three different atomic representations of scaffolded DNA origami 2D lattice structures designed with different mesh patterns.
    • Fig. S19. Exported scalable vector graphics (SVG) schematic of the DNA four-sided polygon.
    • Fig. S20. Exported SVG schematic of the DNA five-sided polygon.
    • Fig. S21. Exported SVG schematic of the DNA six-sided polygon.
    • Fig. S22. Exported SVG schematic of the 42-bp edge-length DNA L-shape wireframe lattice.
    • Fig. S23. Exported SVG schematic of the 63-bp edge-length DNA L-shape wireframe lattice.
    • Fig. S24. Exported SVG schematic of the 84-bp edge-length DNA L-shape wireframe lattice.
    • Fig. S25. Exported SVG schematic of the DNA curved-arm wireframe lattice (quadrilateral meshes).
    • Fig. S26. Exported SVG schematic of the DNA curved-arm wireframe lattice (triangular meshes).
    • Fig. S27. Exported SVG schematic of the DNA curved-arm wireframe lattice (mixed meshes).
    • Fig. S28. AFM imaging of the DNA four-sided polygon wireframe lattice.
    • Fig. S29. AFM imaging of the DNA five-sided polygon wireframe lattice.
    • Fig. S30. AFM imaging of the DNA six-sided polygon wireframe lattice.
    • Fig. S31. AFM imaging of the DNA 42-bp edge-length L-shape DNA wireframe lattice.
    • Fig. S32. AFM imaging of the DNA 63-bp edge-length L-shape wireframe lattice.
    • Fig. S33. AFM imaging of the DNA 84-bp edge-length L-shape DNA wireframe lattice.
    • Fig. S34. AFM imaging of the DNA curved-arm wireframe lattice (quadrilateral meshes).
    • Fig. S35. AFM imaging of the DNA curved-arm wireframe lattice (triangular meshes).
    • Fig. S36. AFM imaging of the DNA curved-arm wireframe lattice (mixed meshes).
    • Fig. S37. Truss-like finite element simulation.
    • Fig. S38. Fifteen target geometries used as input to the algorithm.
    • Fig. S39. Base pair models with the scaffold and staple double crossovers for 15 diverse 2D wireframe lattice structures.
    • Fig. S40. Fifteen spanning trees of the dual graph of the loop-crossover structures generated by the algorithm.
    • Fig. S41. Scaffold-routing path of 15 diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S42. Staple design path of 15 diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S43. Cylindrical representations of 15 diverse 2D wireframe lattice structures.
    • Fig. S44. Atomic models of 15 diverse 2D wireframe lattice structures generated by the algorithm.
    • Fig. S45. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with triangular meshes.
    • Fig. S46. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with quadrilateral meshes.
    • Fig. S47. Three different atomic representations of scaffolded DNA origami 2D wireframe structures with N-polygonal meshes.
    • Fig. S48. Exported SVG schematic of the square wireframe lattice.
    • Fig. S49. Exported SVG schematic of the honeycomb wireframe lattice.
    • Fig. S50. Exported SVG schematic of the DNA rhombic tiling lattice.
    • Fig. S51. Exported SVG schematic of the DNA quarter circle wireframe lattice.
    • Fig. S52. Exported SVG schematic of the DNA Cairo pentagonal tiling.
    • Fig. S53. Exported SVG schematic of the DNA lotus wireframe lattice.
    • Fig. S54. AFM imaging of the DNA square wireframe lattice.
    • Fig. S55. AFM imaging of the DNA honeycomb wireframe lattice.
    • Fig. S56. AFM imaging of the DNA rhombic tiling wireframe lattice.
    • Fig. S57. AFM imaging of the DNA Cairo pentagonal tiling wireframe lattice.
    • Fig. S58. AFM imaging of the DNA lotus wireframe lattice.
    • Table S1. Required scaffold lengths for 24 rendered DNA lattice structures.
    • Table S2. Output from of the automatic sequence design for DNA origami 2D wireframe structures.
    • Table S3. Folding yields determined by counting well-folded particles from AFM imaging.
    • Table S4. Staple sequence for 84-bp edge-length DNA four-sided polygon origami folding.
    • Table S5. Staple sequence for 84-bp edge-length DNA five-sided polygon origami folding.
    • Table S6. Staple sequence for 84-bp edge-length DNA six-sided polygon origami folding.
    • Table S7. Staple sequence for 42-bp edge-length DNA L-shape origami folding.
    • Table S8. Staple sequence for 63-bp edge-length DNA L-shape origami folding.
    • Table S9. Staple sequence for 84-bp edge-length DNA L-shape origami folding.
    • Table S10. Staple sequence for DNA curved-beam origami folding (quadrilateral mesh pattern).
    • Table S11. Staple sequence for DNA curved-beam origami folding (triangular mesh pattern).
    • Table S12. Staple sequence for DNA curved-beam origami folding (mixed mesh pattern).
    • Table S13. Staple sequence for 42-bp edge-length DNA plate origami folding.
    • Table S14. Staple sequence for 42-bp edge-length DNA honeycomb origami folding.
    • Table S15. Staple sequence for 84-bp edge-length DNA rhombic tiling origami folding.
    • Table S16. Staple sequence for DNA quarter circle origami folding.
    • Table S17. Staple sequence for DNA Cairo pentagonal tiling origami folding.
    • Table S18. Staple sequence for DNA lotus origami folding.
    • Table S19. Sequences for the 7249-nt (#1), 5386-nt (#2), and 2267-nt (#3) length scaffolds used.
    • References (4046)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Movie S1 (.mp4 format). PERDIX run.
    • Movie S2 (.mp4 format). PERDIX boundary design.
    • Movie S3 (.mp4 format). PERDIX boundary and internal design.
    • Movie S4 (.mp4 format). Atomic models: Different meshes.
    • Movie S5 (.mp4 format). Atomic models: N-arm.
    • Movie S6 (.mp4 format). Atomic models: L-shape.
    • Movie S7 (.mp4 format). Atomic models: Curved arm.
    • Data file S1 (.zip format). PERDIX software package
    • Data file S2 (.pdf format). PERDIX software documentation

    Files in this Data Supplement:

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