1 / 109

January 18, 2010

Shape Replication through Self-Assembly and Rnase Enzymes . January 18, 2010. Read:. Replicate:. Zachary Abel Harvard University Nadia Benbernou Massachusetts Institute of Technology Mirela Damian Villanova University Erik D. Demaine Massachusetts Institute of Technology

caelan
Download Presentation

January 18, 2010

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Shape Replication through Self-Assembly and Rnase Enzymes January 18, 2010 Read: Replicate: Zachary Abel Harvard University Nadia Benbernou Massachusetts Institute of Technology Mirela Damian Villanova University Erik D. Demaine Massachusetts Institute of Technology Martin Demaine Massachusetts Institute of Technology Robin Flatland Siena College Skott D. Kominers Harvard University Robert Schweller University of Texas Pan American

  2. Outline • Basic Model • RNA enzyme model • Shape replication • Precise yield shape replication • Infinite yield shape replication

  3. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = Glue Function: Tile Set: Temperature:

  4. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d

  5. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d

  6. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d b c

  7. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d b c

  8. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d b c

  9. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d a b c

  10. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d a b c

  11. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d a b c

  12. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d a b c

  13. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e d a b c

  14. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T = e x d a b c

  15. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e e x d a b c G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  16. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e e x x d a b c G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  17. Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e x e x x d a b c G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  18. (Basic)Tile Assembly Model (Rothemund, Winfree, Adleman) a b c x d e x x e x x d a b c G(y) = 2 G(g) = 2 G(r) = 2 G(b) = 2 G(p) = 1 G(w) = 1 t = 2 T =

  19. Outline • Basic Model • RNA enzyme model • Shape replication • Precise yield shape replication • Infinite yield shape replication

  20. RNA enzyme Self-Assembly (suggested by Rothemund, Winfree 2000) All tile types are of either DNA or RNA makeup: RNA tile types DNA tile types • RNA assembly model: • Assembly occurs over a number of stages. • At each stage you may: • 1) Add a new collection of tile types • - Allow for further growth • - All added types have infinite count • 2) Add an Rnaseenzyme • - Dissolve all RNA tile types • - May break apart assemblies

  21. RNA enzyme Self-Assembly Stage 1:

  22. RNA enzyme Self-Assembly Stage 1:

  23. RNA enzyme Self-Assembly Stage 1: Stage 2:

  24. RNA enzyme Self-Assembly Stage 1: Stage 2:

  25. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme

  26. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme

  27. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme

  28. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme Stage 4:

  29. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme Stage 4:

  30. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme Stage 4:

  31. RNA enzyme Self-Assembly Stage 1: Stage 2: Stage 3: Enzyme Stage 4:

  32. RNA enzyme Self-Assembly • Metrics for efficiency: • Tile complexity: total number of distinct tile types used in the system. • Stage complexity: total number of distinct stages used. Stage 1: Stage 2: Stage 3: Enzyme Stage 4:

  33. Outline • Basic Model • RNA enzyme model • Shape replication • Precise yield shape replication • Infinite yield shape replication

  34. Shape Replication Problem Design an assembly system (algorithm) that will replicate a large number of copies given a single copy of a pre-assembled input shape. Precise Yield: Replicate exactly n copies for a given n Infinite Yield: Replicate infinite copies -in practice, the number of copies should only be limited by the volume of particles available.

  35. Outline • Basic Model • RNA enzyme model • Shape replication • Precise yield shape replication • Infinite yield shape replication

  36. Precise Yield: rectangles

  37. Precise Yield: rectangles a a a a a a a a a a a a a a a a a a a a

  38. Precise Yield: rectangles n n n n e w w e w e w e w e w e s s s s

  39. Precise Yield: rectangles x x n y y n n n n w e w w e w e w e w e w e s s s s

  40. Precise Yield: rectangles n w n n n n e w w e w e w e w e w e s s s s

  41. Precise Yield: rectangles n n w e n n n n e w w e w e w e w e w e s s s s e w s s

  42. Precise Yield: rectangles n n e w n n n n e w w e w e w e w e w e s s s s e w s s

  43. Precise Yield: rectangles n n n n e w a e w a e w w e a w e w a w e s s s s

  44. Precise Yield: rectangles Step 1: Coat shape with layer of RNA n n e w w e s s

  45. Precise Yield: rectangles Step 1: Coat shape with layer of RNA Step 2: Coat shape with layer of DNA n n e w w e s s

  46. Precise Yield: rectangles Step 1: Coat shape with layer of RNA. Step 2: Coat shape with layer of DNA. Step 3: Add enzyme.

  47. Precise Yield: rectangles Step 1: Coat shape with layer of RNA. Step 2: Coat shape with layer of DNA. Step 3: Add enzyme.

  48. Precise Yield: rectangles Step 1: Coat shape with layer of RNA. Step 2: Coat shape with layer of DNA. Step 3: Add enzyme. Step 4: Coat frame with layer of RNA.

  49. Precise Yield: rectangles Step 1: Coat shape with layer of RNA. Step 2: Coat shape with layer of DNA. Step 3: Add enzyme. Step 4: Coat frame with layer of RNA.

  50. Precise Yield: rectangles Step 1: Coat shape with layer of RNA. Step 2: Coat shape with layer of DNA. Step 3: Add enzyme. Step 4: Coat frame with layer of RNA. Step 5: Fill frame with DNA.

More Related