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 Open/close Extension/contraction Motivation Motivation-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 track Motivation Motivation-Device I-Device II-Device III-Conclusion

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

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

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

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

Device I: Operation 8 Device I Motivation-Device 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* + CB*C => B + C* A*D => A + D*B*D => B* + D

Device I: Operation 9 Device I Motivation-Device 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* + CB*C => B + C* A*D => A + D*B*D => B* + D

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

Device I: Operation 11 Device I Motivation-Device 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* + CB*C => B + C* A*D => A + D*B*D => B* + D

Device I: Operation 12 Device I Motivation-Device 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* + CB*C => B + C* A*D => A + D*B*D => B* + D

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

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

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

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

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

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

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

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

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

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

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

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 colors For more detail, see our poster.

Acknowledgement 40 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 Andrew J. Turberfield