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