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A Unidirectional DNA Walker Moving Autonomously Along a Track


Peng Yin*, Hao Yan*, Xiaoju G. Daniell*, Andrew J. Turberfield, John H. Reif*
Department

* Department of Computer Science, Duke University of Physics, Clarendon Laboratory, University of Oxford

Motivation
DNA nanorobotics
Rotation, open/close extension/contraction mediated by environmental changes

Autonomous, unidirectional motion along an extended linear track

Kinesin
(R. Cross Lab)

Synthetic unidirectional DNA walker that moves autonomously along a linear route over a macroscopic structure ? (Recent work: non-autonomous DNA walker by Seemans group, Autonomous DNA tweezer by Maos group)

Abstract
A nanoscale object moving autonomously over a self-assembled microscopic structure has important nano-robotics applications, e.g. serving as a nanoparticle 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.

Structural overview

Operational overview

Autonomous Motion of the Walker

Stepwise Motion of the Walker

Unidirectional Motion of the Walker

No B

Unidirectional Motion of the Walker

No B*

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Intramolecular Reactions

No dimer

Dimer control

Monomer control

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Time course

Increase in intensity

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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. Nanorobotics systems of this kind would open new horizons in nano-computing, nano-fabrication, nano-electronics, and nano-diagnostics/therapeutics.