1. Autonomous DNA Walking Devices1
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. Extension/contraction
Motivation-Device I-Device II-Device III-Conclusion 2
Motivation
DNA based nanorobotics devices
Rotation
Open/close
(Mao et al 99)
(Yurke et al 00)
(Simmel et al 01)
(Simmel et al 02)
Extension/contraction
(Yan et al 02)
(Li et al 02)
(Alberti et al 03)
(Feng et al 03)

3. Synthetic unidirectional DNA walker that moves autonomously
Motivation-Device I-Device II-Device III-Conclusion 3
Motivation
DNA nanorobotics
Rotation, open/close
extension/contraction
mediated by
environmental changes
Autonomous, unidirectional motion along an extended linear track
(R. Cross Lab)
Kinesin
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. Motivation-Device I-Device II-Device III-Conclusion4
DNA 101: Enzyme Ligation, Restriction
Sticky ends
DNA ligase
DNA restriction enzyme

5. Motivation-Device I-Device II-Device III-Conclusion5
DNA 101: Enzyme Ligation, Restriction
Sticky ends
DNA ligase
DNA restriction enzyme

6. Motivation-Device I-Device II-Device III-Conclusion6
DNA 101: Enzyme Ligation, Restriction
Sticky ends
DNA ligase
DNA restriction enzyme

7. Motivation-Device I-Device II-Device III-Conclusion7
Device I: Structural overview

8. Motivation-Device I-Device II-Device III-Conclusion8
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

9. Motivation-Device I-Device II-Device III-Conclusion9
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. Motivation-Device I-Device II-Device III-Conclusion10
Device I: Operation

11. Motivation-Device I-Device II-Device III-Conclusion11
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. Motivation-Device I-Device II-Device III-Conclusion12
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. Motivation-Device I-Device II-Device III-Conclusion13
Device I: Operation

14. Motivation-Device I-Device II-Device III-Conclusion14
Device I: Operation

15. Motivation-Device I-Device II-Device III-Conclusion15
Device I: Nanowheel

16. Motivation-Device I-Device II-Device III-Conclusion16
Device I: Dual Nanowheel

17. Motivation-Device I-Device II-Device III-Conclusion17
Device II: Structure overview

18. Motivation-Device I-Device II-Device III-Conclusion18
Device II: Operation

19. Motivation-Device I-Device II-Device III-Conclusion19
Device II: Operation

20. Motivation-Device I-Device II-Device III-Conclusion20
Device II: Operation

21. Motivation-Device I-Device II-Device III-Conclusion21
Device II: Operation

22. Motivation-Device I-Device II-Device III-Conclusion22
Device II: Operation

23. Motivation-Device I-Device II-Device III-Conclusion23
Design III: Structure overview
Ligase
PflM I
BstAP I
Restriction enzymes
Walker *
Anchorage A B C D A
Track

24. DNA Walker: Operation Valid hybridization: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 B C D A
Track

25. DNA Walker: Operation Valid hybridization: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*
Ligase C D A
A*B

26. DNA Walker: Operation Valid hybridization: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*
Ligase C D A
A*B

27. DNA Walker: Operation Valid hybridization: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*
PflM I C D A
A*B

28. DNA Walker: Operation Valid hybridization: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 C D A

29. DNA Walker: Operation Valid hybridization: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*
Ligase D A A
B*C

30. DNA Walker: Operation Valid hybridization:30
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*
Ligase D A A
B*C

31. DNA Walker: Operation Valid hybridization: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*
BstAP I D A A
B*C

32. DNA Walker: Operation Valid hybridization: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 B D A

33. DNA Walker: Operation Valid hybridization: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 A B C

34. DNA Walker: Operation Valid hybridization:34
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

35. DNA Walker: Operation Valid hybridization: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 B C A

36. DNA Walker: Operation Valid hybridization: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* A B C D

37. DNA Walker: Experimental Design37
DNA Walker: Experimental Design

38. 38
DNA Walker:
Experimental Design

39. Autonomous Motion of the Walker39
Autonomous Motion of the Walker
For more detail, see our poster.

40. DNA Turing Machine: Structure40
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.

41. Acknowledgement Duke CS DNA Nano Group Physics, University of Oxford41
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