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DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee

1. DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee Prof. Reif (Advisor), Prof. Agarwal, Prof. Hartemink Prof. LaBean, Prof. Turberfield, Prof. Yan. Nanofabrication. Nanoelectronics. Nanorobotics. Nanodiagnostics/ therapeutics. Nanocomputation. 2.

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DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee

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  1. 1 DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee Prof. Reif (Advisor), Prof. Agarwal, Prof. Hartemink Prof. LaBean, Prof. Turberfield, Prof. Yan

  2. Nanofabrication Nanoelectronics Nanorobotics Nanodiagnostics/ therapeutics Nanocomputation 2 There's Plenty of Room at the Bottom Richard P. Feynman, 1959 • “…a field, in which little has been done, but in which an enormous amount can be done in principle” Nanoworld (1 m = 109nm)

  3. 3 There's Plenty of Room at the Bottom Nanoworld (1 m = 109nm) ?

  4. 4 There's Plenty of Room at the Bottom Nanoworld (1 m = 109nm) How to build things? How to make things move (and do work)? How to compute?

  5. Complementary single strands 3.4 nm Duplex 2 nm 5 DNA 101: DNA – Not merely secret to life • Information encoding: bases: A, T, C, G • Complementarity of bases:A – T; C – G Self-Assembly !

  6. 6 DNA 101: Self-assembly Single strand DNA as Smart glues (Excerpted from Seeman 03)

  7. How to build? How to compute? How to move? DNA Based Self-Assembly Nano-Device Biochem. Lab Fabrication Theoretical Design Mathematical Analysis Computer Modeling 7 DNA Based Self-Assembly & Nano-Device: Theory & Practice Theory & Practice

  8. Complexity - Error Correction – Nanorobotics - Nanocomputing • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device 8 Roadmap: DNA Based Self-Assembly & Nano-Device

  9. Complexity - Error Correction – Nanorobotics - Nanocomputing 9 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  10. Complexity - Error Correction – Nanorobotics - Nanocomputing 10 Self-Assembly Complexity of Graph Self-Assembly in Accretive Systems and Self-Destructible Systems Joint with Reif, Sahu Reif, Sahu, & Yin (2005) Submitted to FNANO 2005

  11. Seed vertex Temperature Graph Weight function Temperature: τ = 2 Seed vertex Complexity - Error Correction – Nanorobotics - Nanocomputing 11 Accretive Graph Assembly System Sequentially constructible?

  12. Complexity - Error Correction – Nanorobotics - Nanocomputing 12 Problems, Results, & Contributions • Problems • Accretive Graph Assembly Problem • Self-Destructible Graph Assembly Prob. • Results • AGAP is NP-complete • Planar AGAP is NP-complete • #AGAP/Stochastic AGAP is #P-complete • DGAP is PSPACE-complete • Contributions • Cooperative effects of attraction and repulsion • General setting of graphs • Dynamic self-destructible behavior in DGAP model

  13. Complexity - Error Correction – Nanorobotics – Nanocomputing 13 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  14. Complexity - Error Correction – Nanorobotics – Nanocomputing 14 Self-Assembly Compact Error Resilient Computational DNA Tilings Joint with Reif, Sahu Reif, Sahu, & Yin (2004) DNA 10

  15. Complexity - Error Correction – Nanorobotics – Nanocomputing Tile (Excerpted from Yan et al 03) Computational tiles (Winfree) Pad Output 2 Output 1 Input 2 Input 1 15 Computational Tilings Output 1 = Input 1 XOR Input 2 Output 2 = Input 1 AND Input 2

  16. Complexity - Error Correction – Nanorobotics – Nanocomputing 16 Binary counter Binary counter Computational tiles Seed tile Frame tiles

  17. Complexity - Error Correction – Nanorobotics – Nanocomputing Error! 17 Error in Assembly Binary counter Computational tiles Seed tile Frame tiles

  18. Complexity - Error Correction – Nanorobotics – Nanocomputing 18 Error Resilient Tilings by Winfree Original tiles: Error resilient tiles: (Excerpted from Winfree 03) • Error rate   2 • Assembly size increased by 4

  19. Complexity - Error Correction – Nanorobotics – Nanocomputing 19 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles:

  20. Complexity - Error Correction – Nanorobotics – Nanocomputing 20 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles:

  21. Complexity - Error Correction – Nanorobotics – Nanocomputing 21 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles: Error checking pads • Assembly size not increased • Two way overlay: error rate (5%)  2 (0.25%) • Three way overlay: error rate  (5%)  3 (0.0125%)

  22. Complexity - Error Correction – Nanorobotics – Nanocomputing 22 Computer Simulation (Xgrow, Winfree) Three way overlay Winfree 3x3 construction Winfree 2x2 construction Two way overlay No error correction

  23. Complexity - Error Correction – Nanorobotics - Nanocomputing 23 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  24. Complexity - Error Correction – Nanorobotics - Nanocomputing (R. Cross Lab) 24 Nano-Device An Autonomous Unidirectional DNA Walker Joint with Yan, Daniell, Turberfield, Reif Yin, Yan, Daniell, Turberfield, & Reif (2004) Angew. Chem. Intl. Ed. Yin, Turberfield, & Reif (2004) DNA 10

  25. Complexity - Error Correction – Nanorobotics - Nanocomputing Restriction enzymes PflM I BstAP I Walker * Ligase 25 Autonomous Unidirectional DNA Walker: Design Anchorage A A B D C Track

  26. Complexity - Error Correction – Nanorobotics - Nanocomputing Sticky ends DNA ligase DNA restriction enzyme 26 DNA 101: Enzyme Ligation, Restriction

  27. Complexity - Error Correction – Nanorobotics - Nanocomputing 27 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* Walker Anchorage * A A B D C Track

  28. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 28 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C D A A*B

  29. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 29 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C D A A*B

  30. Complexity - Error Correction – Nanorobotics - Nanocomputing 30 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* PflM I C D A A*B

  31. Complexity - Error Correction – Nanorobotics - Nanocomputing 31 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* B* A D C A

  32. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 32 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D A A B*C

  33. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 33 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D A A B*C

  34. Complexity - Error Correction – Nanorobotics - Nanocomputing 34 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* BstAP I D A A B*C

  35. Complexity - Error Correction – Nanorobotics - Nanocomputing 35 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C* A D B A

  36. Complexity - Error Correction – Nanorobotics - Nanocomputing 36 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* A C*D B A

  37. Complexity - Error Correction – Nanorobotics - Nanocomputing 37 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D* A C B A

  38. Complexity - Error Correction – Nanorobotics - Nanocomputing 38 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D*A B C A

  39. Complexity - Error Correction – Nanorobotics - Nanocomputing 39 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* A* D C B A

  40. Complexity - Error Correction – Nanorobotics - Nanocomputing 40 DNA Walker: Experimental Design

  41. Complexity - Error Correction – Nanorobotics - Nanocomputing 41 Autonomous Motion of the Walker

  42. Complexity - Error Correction – Nanorobotics - Nanocomputing 42 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  43. Complexity - Error Correction – Nanorobotics - Nanocomputing 43 Nano-Device Designs of DNA Cellular Computing Devices Joint with Sahu, Turberfield, Reif Yin, Turberfield, Sahu, & Reif (2004) DNA 10 Yin, Sahu,Turberfield, & Reif (2005) Submitted to DNA 11

  44. Complexity - Error Correction – Nanorobotics - Nanocomputing 44 DNA Cellular Computing Devices Self-assembly Nanorobotics Nanocomputation (Benenson et al 03) (Yan et al 03) Complex motion Intelligent robotics devices Reusable DNA computers

  45. Complexity - Error Correction – Nanorobotics - Nanocomputing 45 DNA Cellular Computing Devices Finite state automata Turing machine Cellular automata

  46. Complexity - Error Correction – Nanorobotics - Nanocomputing 46 Comp 101: Turing Machine Read/write head Tape Transition rule

  47. Complexity - Error Correction – Nanorobotics - Nanocomputing 47 DNA Turing Machine: Structure Turing machine Transition table: Rule molecules Turing head: Head molecules Data tape: Symbol molecules Autonomous universal DNA Turing machine: 2 states, 5 colors

  48. Complexity - Error Correction – Nanorobotics - Nanocomputing 48 Turing Machine: Operation Turing machine

  49. Complexity - Error Correction – Nanorobotics - Nanocomputing 49 Turing Machine: Operation

  50. Complexity - Error Correction – Nanorobotics - Nanocomputing 50 Turing Machine: Operation

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