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

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