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

1

Motivation

2

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)

Rotation

Rotation

Open/close Open/close Open/close

Extension/contraction Extension/contraction Extension/contraction

MotivationMotivation-Device I-Device II-Device III-Conclusion

Motivation

3

DNA nanorobotics

(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)

Rotation, open/close

extension/contraction

mediated by

environmental changes

Autonomous, unidirectional motion along an extended linear trackAutonomous, unidirectional motion along an extended linear track

MotivationMotivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

4

Sticky ends

DNA ligase

DNA restriction enzyme

MotivationMotivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

5

Sticky ends

DNA ligase

DNA restriction enzyme

MotivationMotivation-Device I-Device II-Device III-Conclusion

DNA 101: Enzyme Ligation, Restriction

6

Sticky ends

DNA ligase

DNA restriction enzyme

MotivationMotivation-Device I-Device II-Device III-Conclusion

Device I: Structural overview

7Motivation-Device IDevice I-Device II-Device III-Conclusion

Device I: Operation

8Motivation-Device IDevice I-Device II-Device III-Conclusion

• 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

Device I: Operation

9Motivation-Device IDevice I-Device II-Device III-Conclusion

• 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

Device I: Operation

10Motivation-Device IDevice I-Device II-Device III-Conclusion

Device I: Operation

11Motivation-Device IDevice I-Device II-Device III-Conclusion

• 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

Device I: Operation

12Motivation-Device IDevice I-Device II-Device III-Conclusion

• 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

Device I: Operation

13Motivation-Device IDevice I-Device II-Device III-Conclusion

Device I: Operation

14Motivation-Device IDevice I-Device II-Device III-Conclusion

Device I: Nanowheel

15Motivation-Device IDevice I-Device II-Device III-Conclusion

Device I: Dual Nanowheel

16Motivation-Device IDevice I-Device II-Device III-Conclusion

Device II: Structure overview

17Motivation-Device I-Device IIDevice II-Device III-Conclusion

Device II: Operation

18Motivation-Device I-Device IIDevice II-Device III-Conclusion

Device II: Operation

19Motivation-Device I-Device IIDevice II-Device III-Conclusion

Device II: Operation

20Motivation-Device I-Device IIDevice II-Device III-Conclusion

Device II: Operation

21Motivation-Device I-Device IIDevice II-Device III-Conclusion

Device II: Operation

22Motivation-Device I-Device IIDevice II-Device III-Conclusion

Design III: Structure overview

23

B C D A

Track

AnchorageA

Walker*

LigasePflM I

BstAP I

Restriction enzymes

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

• 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*

DNA Walker: Operation

24

B C D A

Track

AnchorageA

Walker*

• 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*BAC D

DNA Walker: Operation

25

Ligase

• 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*BAC D

DNA Walker: Operation

26

Ligase

• 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*BAC D

DNA Walker: Operation

27

PflM I

• 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

DNA Walker: Operation

28

• 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*CA

AD

DNA Walker: Operation

29

Ligase

• 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*CA

AD

DNA Walker: Operation

30

Ligase

• 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*CA

AD

DNA Walker: Operation

31

BstAP I

• 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

DNA Walker: Operation

32

• 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*ACA B

DNA Walker: Operation

33

• 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 AA B

DNA Walker: Operation

34

• 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

DNA Walker: Operation

35

• 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

DNA Walker: Operation

36

37

DNA Walker: Experimental Design

38

Autonomous Motion of the Walker

For more detail, see our poster.For more detail, see our poster.

DNA Turing Machine: Structure

39

Turing machine

Transitional rules: Rule molecules

Turing head: Head molecules

Data tape: Symbol molecules

Autonomous universal DNA Turing machine: 2 states, 5 colorsAutonomous universal DNA Turing machine: 2 states, 5 colors

For more detail, see our poster.For more detail, see our poster.

Acknowledgement

40

• Duke CS DNA Nano GroupPeng YinPeng Yin

Hao YanHao 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. TurberfieldAndrew J. Turberfield