AAWSAP DIRD, Quantum Computing and Utilizing Organic Molecules in Automation Technology, December 2010

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landscapes traversed by molecules. The capability for computation is also needed to analyze
these data and, in many applications, some rudimentary processing units such as the logic
gate networks shown in the previous section would be enough to achieve useful
functionalities.
To exhibit these capabilities, a team of scientists from Columbia University, Arizona State
University, the University of Michigan, and the California Institute of Technology (Caltech)
(123) have programmed an autonomous molecular "robot" made out of DNA to start, move,
turn, and stop while following a DNA track. This development could ultimately lead to
molecular systems that might one day be used for medical therapeutic devices and
molecular-scale reconfigurable robots-robots made of many simple units that can reposition
or even rebuild themselves to accomplish different tasks. The researchers constructed a trail
of molecular "bread crumbs" on the DNA origami track by stringing additional single-stranded
DNA molecules, or oligonucleotides, off the ends of the staples. These represent the cues
that tell the molecular robots what to do-start, walk, turn left, turn right, or stop, for
example-akin to the commands given to traditional robots. We will discuss the "nano
walker" in greater detail in a later section in this treatise. It is this third function, the
controlled movement of molecules through the aid of nanometers that will be discussed next.
DNA Nanomotors
Molecular-size motors have evolved in nature, where they are used in virtually every
important biological process. In contrast, the development of synthetic nanometers that
mimic the function of these amazing natural systems and that could be used in man-made
nanodevices is in its infancy. Building nanoscale motors is not just an exercise in scaling
down the design of a macroworld engine to nanoscale dimensions. Many factors such as
friction, heat dissipation and many other mechanical behaviors are just very different at this
scale - everything is constantly moving (under kinetic energy supplied by the heat of the
surroundings) and being buffeted by other atoms and molecules (Brownian motion). The
concept of a single DNA molecule nanometer was already introduced in early 2002. (124)
DNA nanometers are synthetic biochemical devices whose motion can be controlled at the
molecular scale.
DNA molecular motors will be indispensable parts for the construction of molecular robots.
The motion of a robot should be well-controlled by means of some molecular input, or it
should be driven autonomously by cues from the environment. First approaches to encode
molecular motion in DNA structures were based on the reversible and input-sensitive
conformational changes. For example, the first reported use of a DNA motor was a
nanomechanical device which generated twisting motion along the helix axis based on 8-Z
transition controlled by ionic strength of a solution. (125) Then, the first molecular tweezers
were driven by successive reversible branch migrations of DNA strands, and these strands
were called "fuel" and "anti-fuel." (126) The next level in complexity were "remotely­
controlled" walkers introduced by Seeman and Pierce, as they were based on a series of
successive unidirectional conformational changes driven by strand displacement. These
sequential conformational changes were microscopic analogs of macroscopic commands such
as: "lift the first leg", "drop the first leg to the next available position"; "lift the second leg",
"drop the second leg to the next available position", with a cumulative result of a
translational movement of a molecule along a track. One drawback of these systems was
that they were not autonomous, and that each conformational change had to be triggered
separately, while one advantage was that they could have been monitored easily in bulk with
fluorescence measurements. The first autonomous systems were based on nucleic acid
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