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Autonomous DNA Walking Devices Peng Yin*, Andrew J. Turberfield † , Hao Yan*, John H. Reif* * Department of Computer PowerPoint Presentation
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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.

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slide1

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

slide2

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)

slide3

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)

slide4

4

Motivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

Sticky ends

DNA ligase

DNA restriction enzyme

slide5

5

Motivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

Sticky ends

DNA ligase

DNA restriction enzyme

slide6

6

Motivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

Sticky ends

DNA ligase

DNA restriction enzyme

slide7

7

Motivation-Device I-Device II-Device III-Conclusion

Device I: Structural overview

slide8

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
slide9

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
slide10

10

Motivation-Device I-Device II-Device III-Conclusion

Device I: Operation

slide11

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
slide12

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
slide13

13

Motivation-Device I-Device II-Device III-Conclusion

Device I: Operation

slide14

14

Motivation-Device I-Device II-Device III-Conclusion

Device I: Operation

slide15

15

Motivation-Device I-Device II-Device III-Conclusion

Device I: Nanowheel

slide16

16

Motivation-Device I-Device II-Device III-Conclusion

Device I: Dual Nanowheel

slide17

17

Motivation-Device I-Device II-Device III-Conclusion

Device II: Structure overview

slide18

18

Motivation-Device I-Device II-Device III-Conclusion

Device II: Operation

slide19

19

Motivation-Device I-Device II-Device III-Conclusion

Device II: Operation

slide20

20

Motivation-Device I-Device II-Device III-Conclusion

Device II: Operation

slide21

21

Motivation-Device I-Device II-Device III-Conclusion

Device II: Operation

slide22

22

Motivation-Device I-Device II-Device III-Conclusion

Device II: Operation

slide23

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

slide24

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

slide25

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

slide26

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

slide27

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

slide28

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

slide29

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

slide30

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

slide31

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

slide32

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

slide33

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

slide34

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

slide35

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

slide36

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

slide37

37

DNA Walker: Experimental Design

slide38

38

Autonomous Motion of the Walker

For more detail, see our poster.

slide39

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.

slide40

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