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

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Motivation

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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 walker 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 trackAutonomous, unidirectional motion along an extended linear track

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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.

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Structural overview

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Operational overview

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Autonomous Motion of the Walker

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Stepwise Motion of the Walker

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Unidirectional Motion of the Walker

No B

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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. Nano-robotics systems of this kind would open new horizons in nano-

computing, nano-fabrication, nano-electronics, and nano-diagnostics/therapeutics.