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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 (40–46)

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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

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