Science Advances
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)
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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