Nanomachine made from DNA nanorings

Researchers from the USA, University of Bonn and the research institute Caesar in Bonn have used nanostructures to construct a tiny machine that constitutes a rotatory motor and can move in a specific direction. The researchers used circular structures from DNA.

Above – The two rings are linked like a chain and can well be recognized. At the center there is the T7 RNA Polymerase. CREDIT (c) Julián Valero

used structures made of DNA nanorings. The two rings are linked like a chain. “One ring fulfills the function of a wheel, the other drives it like an engine with the help of chemical energy”, explains Prof. Dr. Michael Famulok from the Life & Medical Sciences (LIMES) Institute of the University of Bonn.

The tiny vehicle measures only about 30 nanometers (millionths of a millimeter). The “fuel” is provided by the protein “T7 RNA polymerase”. Coupled to the ring that serves as an engine, this enzyme synthesizes an RNA strand based on the DNA sequence and uses the chemical energy released during this process for the rotational movement of the DNA ring. “As the rotation progresses, the RNA strand grows like a thread from the RNA polymerase”, reports lead author Dr. Julián Valero from Famulok’s team. The researchers are using this ever-expanding RNA thread, which basically protrudes from the engine as a waste product, to keep the tiny vehicle on its course by using markings on a DNA-nanotube track.

Length of the test drive is 240 nanometers

Attached to this thread, the unicycle machine covered about 240 nanometers on its test drive. “That was a first go”, says Famulok. “The track can be extended as desired.” In the next step the researchers are not only aiming at expanding the length of the route, but also plan more complex challenges on the test track. At built-in junctions, the nanomachine should decide which way to go. “We can use our methods to predetermine which turn the machine should take”, says Valero with a view towards the future.

Of course, the scientists cannot watch the tiny vehicle at work with the naked eye. By using an atomic force microscope that scanned the surface structure of the nanomachine, the scientists were able to visualize the interlocked DNA rings. In addition, the team used fluorescent markers to show that the “wheel” of the machine was actually turning. Fluorescent “waymarkers” along the nanotube path lit up as soon as the nano-unicycle passed them. Based thereupon, the speed of the vehicle could also be calculated: One turn of the wheel took about ten minutes. That’s not very fast, but nevertheless a big step for the researchers. “Moving the nanomachine in the desired direction is not trivial”, says Famulok.

The components of the machine assemble by self-organization

Of course, unlike macroscopic machines, the nanomachine was not assembled with a welding torch or wrench. The construction is based on the principle of self-organization. As in living cells, the desired structures arise spontaneously when the corresponding components are made available. “It works like an imaginary puzzle”, explains Famulok. Each puzzle piece is designed to interact with very specific partners. If you bring together exactly these partners in a single vessel, each particle will find its partner and the desired structure is automatically created.

By now, scientists worldwide have developed numerous nanomachines and nanoengines. But the method developed by Famulok’s team is a completely novel principle. “This is a big step: It is not easy to reliably design and realize such a thing on a nanometer scale”, says the scientist. His team wants to develop even more complex nanoengine systems soon. “This is basic research”, says Famulok. “It is not possible to see exactly where it will lead.” With some imagination, possible applications could for instance include molecular computers that perform logical operations based on molecular movements. Additionally, tiny machines could transport drugs through the bloodstream precisely to where they are required. “But these are still visions of the future”, says Famulok.

Nature Nanotechnology – A bio-hybrid DNA rotor–stator nanoengine that moves along predefined tracks

Abstract

Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor–stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.

Previously developed nanocars by other researchers

The nanocar is a molecule designed in 2005 at Rice University by a group headed by Professor James Tour. Despite the name, the original nanocar does not contain a molecular motor, hence, it is not really a car. Rather, it was designed to answer the question of how fullerenes move about on metal surfaces; specifically, whether they roll or slide (they roll).

The molecule consists of an H-shaped ‘chassis’ with fullerene groups attached at the four corners to act as wheels.

When dispersed on a gold surface, the molecules attach themselves to the surface via their fullerene groups and are detected via scanning tunneling microscopy. One can deduce their orientation as the frame length is a little shorter than its width.

Upon heating the surface to 200 °C the molecules move forward and back as they roll on their fullerene “wheels”. The nanocar is able to roll about because the fullerene wheel is fitted to the alkyne “axle” through a carbon-carbon single bond. The hydrogen on the neighboring carbon is no great obstacle to free rotation. When the temperature is high enough, the four carbon-carbon bonds rotate and the car rolls about. Occasionally the direction of movement changes as the molecule pivots.

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