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April 4, 2007

Programmable Self-Assembly: How to Harness (Enslave) DNA. April 4, 2007. Robert Schweller Electrical Engineering and Computer Science Department Northwestern University Email: schwellerr@cs.northwestern.edu http://www.cs.northwestern.edu/~schwellerr/. Molecular Building Blocks. T G C G.

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April 4, 2007

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  1. Programmable Self-Assembly: How to Harness (Enslave) DNA April 4, 2007 Robert SchwellerElectrical Engineering and Computer Science Department Northwestern University Email: schwellerr@cs.northwestern.edu http://www.cs.northwestern.edu/~schwellerr/

  2. Molecular Building Blocks T G C G A C G C

  3. Molecular Building Blocks [Reif’s Group, Duke University]

  4. DNA Scaffolding [Sung Ha Park, Constantin Pistol, Sang Jung Ahn, John H. Reif, Alvin R. Lebeck, Chris Dwyer, and Thomas H. LaBean, 2006]

  5. Self-Assembly for Circuit Patterns [Cook, Rothemund, and Winfree, 2003]

  6. More Examples of DNA Tiles [Winfree’s Group, Cal Tech]

  7. 2D Self-Assembly for Turing Machines [Winfree, Yang, and Seeman, 1998]

  8. Simulation of Cellular Automata Paul Rothemund, Nick Papadakis, Erik Winfree, PLoS Biology 2: e424 (2004) 340nm

  9. [Shaw, University of Southern California] Example of 3D Self-Assembly

  10. 3D DNA Cube [Seeman, New York University]

  11. 3D DNA Truncated Octahedron [Seeman, New York University]

  12. Clonable DNA Octahedron [Shih, Quispe, Joyce, 2004]

  13. Outline • Background, Motivation • Model • Temperature Programming • Probabilistic Programming

  14. Tile Model of Self-Assembly (Rothemund, Winfree STOC 2000) Tile System: t : temperature, positive integer G: glue function T: tileset s: seed tile

  15. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  16. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  17. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  18. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  19. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  20. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  21. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  22. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  23. How a tile system self assembles G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  24. Each Shape Requires a Distinct Tile Set

  25. Programmable, General Purpose Tile Set?

  26. Programmable, General Purpose Tile Set? . . .

  27. Outline • Background, Motivation • Model • Temperature Programming • Probabilistic Programming

  28. Multiple Temperature Model Multiple Temperature Model - temperature may go up and down

  29. Multiple Temperature Model Multiple Temperature Model - temperature may go up and down t < t1 , t2 , ... , tr-1 , tr >

  30. Multiple Temperature Model Multiple Temperature Model - temperature may go up and down t < t1 , t2 , ... , tr-1 , tr > Tile Complexity: Number of Tiles Temperature Complexity: Number of Temperatures

  31. Building k x n Rectangles k-digit, base n(1/k) counter: k n

  32. Building k x n Rectangles k-digit, base n(1/k) counter: k n Tile Complexity:

  33. Build a 4 x 256 rectangle: t = 2 S3 0 S2 0 S1 0 S g g g p C0 C1 C2 C3 S

  34. Build a 4 x 256 rectangle: t = 2 S3 0 g S2 0 0 1 2 3 0 0 g S1 0 S g g g p C0 C1 C2 C3 0 S3 0 S2 0 0 S1 g g p S C1 C2 C3

  35. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 g S1 0 S g g g p C0 C1 C2 C3 S3 0 0 S2 0 0 S1 0 0 p S C1 C2 C3

  36. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 g S1 0 S g g g p C0 C1 C2 C3 S3 0 0 S2 0 0 g g S1 0 0 0 1 S C1 C2 C3

  37. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 g S1 0 S g g g p C0 C1 C2 C3 S3 0 0 0 0 S2 0 0 0 0 S1 0 0 0 1 p S C1 C2 C3 C0 C1 C2 C3

  38. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 S g g g p 2 3 C0 C1 C2 C3 S3 0 0 0 0 0 0 S2 0 0 0 0 0 0 S1 0 0 0 1 1 1 p S C1 C2 C3 C0 C1 C2 C3

  39. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 p S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3

  40. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3

  41. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3

  42. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P R S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3

  43. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P R … S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2

  44. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 S3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 S2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 … S1 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P R 0 0 S C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2

  45. Build a 4 x 256 rectangle: t = 2 g g 0 1 0 1 S3 0 p r g S2 0 0 1 2 3 0 0 1 2 g S1 0 p r S P R g g g p 3 0 2 3 p r C0 C1 C2 C3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 P 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 P 3 3 P R 0 0 0 1 1 1 1 2 2 2 2 3 3 3 P C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3 C0 C1 C2 C3

  46. Building k x n Rectangles k-digit, base n(1/k) counter: k n Tile Complexity:

  47. two temperatures t= 4 3 1 3 3 n

  48. two temperatures t = 4 6 n

  49. two temperatures t = 4 6 n Tile Complexity: j = log n / (log log n – log log log n)

  50. t = 4 6 n two temperatures

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