A Unidirectional DNA Walker Moving Autonomously Along a Track

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

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Motivation
DNA nanorobotics
Rotation, open/close extension/contraction mediate
d 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 Seemans
group, Autonomous DNA tweezer by Maos group)
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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
Dimer control
No dimer
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/transporta
tion network. Nano-robotics systems of this kind
would open new horizons in nano-computing,
nano-fabrication, nano-electronics, and
nano-diagnostics/therapeutics.