dna origami design with c adnano t ool k it ctk
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DNA origami design with C aDNAno T ool K it ( CTK ) Tural Aksel - PowerPoint PPT Presentation

Oct 11, 2022 •523 likes •1.44k views

DNA origami design with C aDNAno T ool K it ( CTK ) Tural Aksel Douglas Lab 2018-09-25 DNA origami design with CTK 1 2 3 4 5 6 7 8 9 10 11 12 A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 A B C D E F G H DNA

  1. DNA origami design with C aDNAno T ool K it ( CTK ) Tural Aksel Douglas Lab 2018-09-25

  2. DNA origami design with CTK 1 2 3 4 5 6 7 8 9 10 11 12 A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 A B C D E F G H

  3. DNA origami design with CTK 12 12 11 11 10 10 9 9 8 8 7 7 6 6 5 5 4 4 3 3 2 2 1 1 A D G H A D G H B C B C E F E F origamisim autopipette autobreak

  4. Designing DNA origami using Cadnano

  5. design.json design_autobreak.json CTK autobreak origamisim autopipette

  6. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 3 1 1 3 2 1 1 3 3 3 3 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  7. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  8. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 3 1 1 3 2 1 1 3 3 3 3 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  9. design.json CTK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 autobreak 0 1 1 1 1 1 1 1 1 0 0 0 0 0 2 2 0 10 10 0 0 10 10 1 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 1 3 2 1 1 3 3 3 4 4 2 2 8 8 2 8 8 origamisim 3 2 4 4 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 5 5 autopipette 8 8 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 3 3 10 10 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 1 1 10 11 10 10

  10. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  11. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 3 1 1 3 2 1 1 3 3 3 3 4 4 4 4 4 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 3 3 5 3 3 5 5 3 3 5 5 5 5 3 3 5 5 3 3 5 3 3 5 5 3 3 5 3 3 5 4 3 3 5 5 5 5 3 5 5 3 3 3 3 5 5 4 4 4 4 4 4 4 4 6 6 5 4 6 6 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  12. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  13. design.json CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  14. graph representation CTK autobreak 3' 5' origamisim autopipette

  15. graph representation CTK autobreak 3' 5' origamisim autopipette

  16. possible solution 1 CTK autobreak 3' 5' origamisim autopipette

  17. possible solution 1 CTK autobreak 3' 5' ω 4 ω 1 ω 3 origamisim ω 2 autopipette

  18. possible solution 2 CTK autobreak 3' 5' ω ω 1 6 origamisim ω 2 ω 5 autopipette

  19. shortest path CTK autobreak 3' 5' ω ω 1 6 origamisim ω 2 ω 5 ω 1 ω 2 ω 5 ω S= + + + 6 autopipette

  20. graph representation CTK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 autobreak 3' 1 1 1 1 1 1 1 1 0 0 0 0 0 2 2 0 10 10 0 0 10 10 5' 1 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 1 3 2 1 1 3 3 3 4 4 2 2 8 8 2 8 8 3 2 4 4 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 5 5 origamisim 8 8 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 3 3 10 10 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 1 1 10 11 10 10 5' 3' autopipette

  21. graph representation CTK autobreak 3' 5' origamisim 5' 3' autopipette

  22. graph representation CTK autobreak 3' 5' origamisim 5' 3' autopipette

  23. graph representation CTK autobreak 3' 5' origamisim 5' 3' autopipette

  24. edge weights CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10 Martin TG, Dietz H. (2012)

  25. edge weights CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  26. hybridization CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

  27. hybridization loop closure CTK 1 1 autobreak 0 1 1 1 1 2 2 2 2 2 2 2 0 0 10 10 0 0 10 10 1 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 1 1 3 1 1 3 3 1 1 3 3 3 3 1 1 3 3 1 1 3 1 1 3 3 1 1 3 1 1 3 2 1 1 3 3 3 3 1 3 3 1 1 1 1 3 3 2 2 2 2 4 4 2 2 8 8 2 2 8 8 origamisim 3 2 4 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 5 3 3 5 4 3 3 5 5 5 5 4 4 4 4 6 6 5 4 6 6 4 7 5 5 7 6 7 7 5 5 autopipette 8 8 6 6 7 6 8 8 6 9 7 7 9 8 7 7 3 3 9 9 3 3 10 10 8 8 9 8 10 10 8 11 9 9 11 10 9 9 1 1 11 11 1 1 10 10 11 10 10

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