Autonomous DNA Walking Devices
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1 1 utonomous DN Walking Devices Peng Yin*, ndrew J. Turberfield, Hao Yan*, John H. Reif* * Department of Computer Science, Duke University Department of Physics, Clarendon Laboratory, University of Oxford
2 Motivation Rotation Motivation-Device I-Device II-Device III-Conclusion DN based nanorobotics devices Open/close Open/close Open/close 2 (Mao et al 99) (Yurke et al 00) (Simmel et al 01) (Simmel et al 02) Rotation Extension/contraction Extension/contraction Extension/contraction (Yan et al 02) (Li et al 02) (lberti et al 03) (Feng et al 03)
3 Motivation-Device I-Device II-Device III-Conclusion 3 Motivation DN nanorobotics Rotation, open/close extension/contraction mediated by environmental changes utonomous, unidirectional motion along an extended linear track Kinesin (R. Cross Lab) Synthetic unidirectional DN walker that moves autonomously along a linear route over a macroscopic structure? (Recent work: non-autonomous DN walking device by Seeman s group, autonomous DN tweezer by Mao s group)
4 Motivation-Device I-Device II-Device III-Conclusion DN 101: Enzyme Ligation, Restriction 4 Sticky ends DN ligase DN restriction enzyme
5 Motivation-Device I-Device II-Device III-Conclusion DN 101: Enzyme Ligation, Restriction 5 Sticky ends DN ligase DN restriction enzyme
6 Motivation-Device I-Device II-Device III-Conclusion DN 101: Enzyme Ligation, Restriction 6 Sticky ends DN ligase DN restriction enzyme
7 Motivation-Device I-Device I II-Device III-Conclusion Device I: Structural overview 7
8 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 8 Valid hybridization: + C* *C B* + C B*C * + D *D B + D* B*D Valid cut: *C * + C B*C B + C* *D + D* B*D B* + D
9 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 9 Valid hybridization: + C* *C B* + C B*C * + D *D B + D* B*D Valid cut: *C * + C B*C B + C* *D + D* B*D B* + D
10 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 10
11 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 11 Valid hybridization: + C* *C B* + C B*C * + D *D B + D* B*D Valid cut: *C * + C B*C B + C* *D + D* B*D B* + D
12 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 12 Valid hybridization: + C* *C B* + C B*C * + D *D B + D* B*D Valid cut: *C * + C B*C B + C* *D + D* B*D B* + D
13 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 13
14 Device I: Operation Motivation-Device I-Device I II-Device III-Conclusion 14
15 Device I: Nanowheel Motivation-Device I-Device I II-Device III-Conclusion 15
16 Motivation-Device I-Device I II-Device III-Conclusion Device I: Dual Nanowheel 16
17 Motivation-Device I-Device II-Device III-Conclusion Device II: Structure overview 17
18 Device II: Operation Motivation-Device I-Device II-Device III-Conclusion 18
19 Device II: Operation Motivation-Device I-Device II-Device III-Conclusion 19
20 Device II: Operation Motivation-Device I-Device II-Device III-Conclusion 20
21 Device II: Operation Motivation-Device I-Device II-Device III-Conclusion 21
22 Device II: Operation Motivation-Device I-Device II-Device III-Conclusion 22
23 Motivation-Device I-Device II-Device III-Conclusion Design III: Structure overview 23 Restriction enzymes Ligase PflM I Walker * nchorage B C D BstP I Track
24 24 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * Walker * B nchorage C D Track
25 25 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * Ligase *B C D
26 26 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * Ligase *B C D
27 27 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * PflM I *B C D
28 28 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * B* C D
29 29 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * Ligase B*C D
30 30 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * Ligase B*C D
31 31 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * BstP I B*C D
32 32 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * C* B D
33 33 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * B C D*
34 34 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * B C*D
35 35 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * D* B C
36 36 DN Walker: Operation Valid hybridization: * + B = + B* *B B* + C = B + C* B*C C* + D = C + D* C*D D* + = D + * D* Valid cut: *B + B* B*C B + C* C*D C + D* D* D + * * B C D
37 DN Walker: Experimental Design 37
38 utonomous Motion of the Walker 38 For more detail, see our poster.
39 39 DN Turing Machine: Structure Turing machine Transitional rules: Rule molecules Turing head: Head molecules Data tape: Symbol molecules utonomous universal DN Turing machine: 2 states, 5 colors For more detail, see our poster.
40 40 cknowledgement Duke CS DN Nano Group Peng Yin Hao Yan Xiaoju G. Daniell Thomas H. LaBean Sung Ha Park Sang Jung hn Hanying Li Liping Feng Sudheer Sahu Physics, University of Oxford ndrew J. Turberfield Funding NSF, DRP grants to John H. Reif NSF grant to Hao Yan
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