Autonomous DNA Walking Devices 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

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)

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)

Motivation-Device I-Device II-Device III-Conclusion 4 DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme

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

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

Motivation-Device I-Device II-Device III-Conclusion 7 Device I: Structural overview

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

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

Motivation-Device I-Device II-Device III-Conclusion 10 Device I: Operation

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

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

Motivation-Device I-Device II-Device III-Conclusion 13 Device I: Operation

Motivation-Device I-Device II-Device III-Conclusion 14 Device I: Operation

Motivation-Device I-Device II-Device III-Conclusion 15 Device I: Nanowheel

Motivation-Device I-Device II-Device III-Conclusion 16 Device I: Dual Nanowheel

Motivation-Device I-Device II-Device III-Conclusion 17 Device II: Structure overview

Motivation-Device I-Device II-Device III-Conclusion 18 Device II: Operation

Motivation-Device I-Device II-Device III-Conclusion 19 Device II: Operation

Motivation-Device I-Device II-Device III-Conclusion 20 Device II: Operation

Motivation-Device I-Device II-Device III-Conclusion 21 Device II: Operation

Motivation-Device I-Device II-Device III-Conclusion 22 Device II: Operation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

DNA Walker: Experimental Design 37 DNA Walker: Experimental Design

38 DNA Walker: Experimental Design

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

DNA Turing Machine: Structure 40 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.

Acknowledgement Duke CS DNA Nano Group Physics, University of Oxford 41 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