A Unidirectional DNA Walker Moving Autonomously Along a Track

1. 1 A Unidirectional DNA Walker Moving Autonomously Along a Track Peng Yin*, Hao Yan*, Xiaoju G. Daniell*, Andrew J. Turberfield†, John H. Reif* * Department of Computer Science, Duke University † Department of Physics, Clarendon Laboratory, University of Oxford

2. Kinesin (R. Cross Lab) 2 Motivation DNA nanorobotics Rotation, open/close extension/contraction mediated by environmental changes Autonomous, unidirectional motion along an extended linear track Synthetic unidirectional DNA walker that moves autonomously along a linear route over a macroscopic structure ? (Recent work: non-autonomous DNA walker by Seeman’s group, Autonomous DNA tweezer by Mao’s group)

3. 3 Abstract A nanoscale object moving autonomously over a self-assembled microscopic structure has important nano-robotics applications, e.g. serving as a nano-particle and/or information carrier. Recent successes in self-assembly of DNA nanostructuresprovide a solid structural basis to meet this challenge. However, existing nanoscale synthetic DNA devices are unsuitable for the above purpose: they only exhibit localized non-extensible motions (open/close, extension/contraction, and reversible rotation), mediated by external environmental changes. Here we report an experimental construction of unidirectional DNA walker that moves autonomously along a linear DNA track. The self-assembled track contains three anchorages at which the walker, a six-nucleotide DNA fragment, can be attached. At each step the walker is ligated to the next anchorage, then cut from the previous one by a restriction endonuclease. Each cut destroys the previous restriction site and each ligation creates a new site in such a way that the walker cannot move backwards. The device is powered by the hydrolysis of ATP by T4 ligase. The prototype device can be embedded in other self-assembled DNA structures and in principle be extended beyond 3-step operation.

4. 4 Structural overview

5. 5 Operational overview

6. 6 Autonomous Motion of the Walker

7. 7 Stepwise Motion of the Walker

8. 8 Unidirectional Motion of the Walker No B

9. 9 Unidirectional Motion of the Walker No B*

10. 10 Intramolecular Reactions Dimer control No dimer Monomer control

11. 11 Time course Increase in intensity

12. 12 Conclusion & Discussion In summary, we have designed and constructed a nanoscale device in which an autonomous walker moves unidirectionally along a DNA track, driven by the hydrolysis of ATP. The motion of the walker in principle can be extended well beyond the 3-step system demonstrated here. Discovery of new endonucleases with a larger spacing region between its recognition sequences could lead to walkers of larger sizes. By encoding information into the walker and the anchorages, the device can be extended into a powerful autonomous computing device (and hence an “intelligent” robotics device). It is also possible to embed multiple walking devices in a microscopic self-assembled DNA latticesuch that each walker moves autonomously along its own programmed route and serves as an information and/or nano-particle carrier. Collectively they would produce a complicated pattern of motion and possibly form a coordinated and sophisticated signaling/transportation network. Nano-robotics systems of this kind would open new horizons in nano-computing, nano-fabrication, nano-electronics, and nano-diagnostics/therapeutics.