1 / 40

Autonomous DNA Walking Devices Peng Yin*, Andrew J. Turberfield † , Hao Yan*, John H. Reif*

1. Autonomous DNA Walking Devices Peng Yin*, Andrew J. Turberfield † , Hao Yan*, John H. Reif* * Department of Computer Science, Duke University † Department of Physics, Clarendon Laboratory, University of Oxford. Rotation. Open/close. Open/close. Open/close. Extension/contraction.

hund
Download Presentation

Autonomous DNA Walking Devices Peng Yin*, Andrew J. Turberfield † , Hao Yan*, John H. Reif*

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. 1 Autonomous DNA Walking Devices Peng Yin*, Andrew J. Turberfield†, Hao Yan*, John H. Reif* * Department of Computer Science, Duke University † Department of Physics, Clarendon Laboratory, University of Oxford

  2. Rotation Open/close Open/close Open/close Extension/contraction Extension/contraction Rotation Extension/contraction 2 Motivation-Device I-Device II-Device III-Conclusion Motivation DNA based nanorobotics devices (Mao et al 99) (Yurke et al 00) (Simmel et al 01) (Simmel et al 02) (Yan et al 02) (Li et al 02) (Alberti et al 03) (Feng et al 03)

  3. Kinesin (R. Cross Lab) 3 Motivation-Device I-Device II-Device III-Conclusion Motivation DNA nanorobotics Rotation, open/close extension/contraction mediated by environmental changes Autonomous, unidirectional motion along an extended linear track Synthetic unidirectional DNA walker that moves autonomously along a linear route over a macroscopic structure ? (Recent work: non-autonomous DNA walking device by Seeman’s group, autonomous DNA tweezer by Mao’s group)

  4. 4 Motivation-Device I-Device II-Device III-Conclusion DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme

  5. 5 Motivation-Device I-Device II-Device III-Conclusion DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme

  6. 6 Motivation-Device I-Device II-Device III-Conclusion DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme

  7. 7 Motivation-Device I-Device II-Device III-Conclusion Device I: Structural overview

  8. 8 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation • Valid hybridization: • A + C* => A*CB* + C => B*C • A* + D => A*DB + D* => B*D • Valid cut: • A*C => A* + C B*C => B + C* • A*D => A + D* B*D => B* + D

  9. 9 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation • Valid hybridization: • A + C* => A*C B* + C => B*C • A* + D => A*D B + D* => B*D • Valid cut: • A*C => A* + C B*C => B + C* • A*D => A + D* B*D => B* + D

  10. 10 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation

  11. 11 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation • Valid hybridization: • A + C* => A*C B* + C => B*C • A* + D => A*D B + D* => B*D • Valid cut: • A*C => A* + C B*C => B + C* • A*D => A + D* B*D => B* + D

  12. 12 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation • Valid hybridization: • A + C* => A*C B* + C => B*C • A* + D => A*D B + D* => B*D • Valid cut: • A*C => A* + C B*C => B + C* • A*D => A + D* B*D => B* + D

  13. 13 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation

  14. 14 Motivation-Device I-Device II-Device III-Conclusion Device I: Operation

  15. 15 Motivation-Device I-Device II-Device III-Conclusion Device I: Nanowheel

  16. 16 Motivation-Device I-Device II-Device III-Conclusion Device I: Dual Nanowheel

  17. 17 Motivation-Device I-Device II-Device III-Conclusion Device II: Structure overview

  18. 18 Motivation-Device I-Device II-Device III-Conclusion Device II: Operation

  19. 19 Motivation-Device I-Device II-Device III-Conclusion Device II: Operation

  20. 20 Motivation-Device I-Device II-Device III-Conclusion Device II: Operation

  21. 21 Motivation-Device I-Device II-Device III-Conclusion Device II: Operation

  22. 22 Motivation-Device I-Device II-Device III-Conclusion Device II: Operation

  23. Restriction enzymes PflM I BstAP I Walker * Ligase 23 Motivation-Device I-Device II-Device III-Conclusion Design III: Structure overview Anchorage A A B D C Track

  24. 24 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

  25. Ligase 25 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

  26. Ligase 26 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

  27. 27 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

  28. 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* B* A D C A

  29. Ligase 29 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

  30. Ligase 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* D A A B*C

  31. 31 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

  32. 32 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

  33. 33 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

  34. 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* A C*D B A

  35. 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* D* A C B A

  36. 36 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

  37. 37 DNA Walker: Experimental Design

  38. 38 Autonomous Motion of the Walker For more detail, see our poster.

  39. 39 DNA Turing Machine: Structure Turing machine Transitional rules: Rule molecules Turing head: Head molecules Data tape: Symbol molecules Autonomous universal DNA Turing machine: 2 states, 5 colors For more detail, see our poster.

  40. 40 Acknowledgement • Duke CS DNA Nano Group • Peng Yin • Hao Yan • Xiaoju G. Daniell • Thomas H. LaBean • Sung Ha Park • Sang Jung Ahn • Hanying Li • Liping Feng • Sudheer Sahu • Funding • NSF, DARPA grants to John H. Reif • NSF grant to Hao Yan • Physics, University of Oxford • Andrew J. Turberfield

More Related