1. A Unidirectional DNA Walker Moving Autonomously Along a Track1
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. Synthetic unidirectional DNA walker that moves autonomously2
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 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 nanostructures provide 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. Autonomous Motion of the Walker6
Autonomous Motion of the Walker

7. Stepwise Motion of the Walker7
Stepwise Motion of the Walker

8. Unidirectional Motion of the Walker8
Unidirectional Motion of the Walker
No B

9. Unidirectional Motion of the Walker9
Unidirectional Motion of the Walker
No B*

10. Intramolecular Reactions10
Intramolecular Reactions
Dimer control
No dimer
Monomer control

11. 11
Time course
Increase in intensity

12. Conclusion & Discussion12
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 lattice such 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.