An international team of scientists recently developed a new nanoengine made from DNA. It is powered by an ingenious mechanism that allows for pulsating movement. The researchers are now planning to equip it with a coupler and use it as a driver for complex nanomachines. Their research results were published in the journal Nature Nanotechnology on October 19.
Petr Šulc, an assistant professor in Arizona State University's School of Molecular Sciences and the Biodesign Center for Molecular Design and Biomimetics, collaborated on the project with Professor Famulok (project leader) from the University of Bonn, Germany, and Professor Walter from the University of Michigan.
Šulc used his research group's computer modeling tools to gain insight into the design and operation of this leaf-spring nanoengine. The structure consists of nearly 14,000 nucleotides, which form the basic building blocks of DNA.
Šulc explains: "Without oxDNA, the computer model used by our group to design DNA nanostructures, it would have been impossible to simulate the motion of such large nanostructures. This is the first time that a chemically driven DNA nanotechnology motor has been successfully designed. We are pleased that our research method has contributed to its study and look forward to making more complex nanodevices in the future."
This new engine is similar to a hand grip trainer and can enhance grip strength with regular use. However, this engine is about a million times smaller. The two handles are connected in a V-shaped structure by springs.
In a hand grip trainer, the handles are squeezed together under the resistance of a spring. Once you let go, a spring pushes the handle back into place. "Our motor uses a very similar principle," said Professor Michael Famulok from the Institute of Life and Medical Sciences (LIMES) at the University of Bonn. "But the handles are not pressed together, but pulled together."
Researchers have repurposed a mechanism without which there would be no plants or animals on Earth. Each cell is equipped with a library. It contains the blueprints for the various types of proteins that each cell needs to perform its functions. If a cell wants to produce a certain type of protein, it makes a copy of the corresponding blueprint. This transcript is produced by an enzyme called RNA polymerase.
The original blueprint consists of long strands of DNA. RNA polymerase moves along these strands, copying the stored information letter by letter. "We attached the RNA polymerase to a handle on the nanomachine," explains Famulok, who is also a member of the interdisciplinary research areas "Life and Health" and "Matter" at the University of Bonn. "Between the two handles, we also have a DNA strand tightly connected. The polymerase grabs this strand and copies it. It pulls itself along the chain, and the parts that are not copied become smaller and smaller. This pulls the second handle toward the first handle little by little, compressing the spring at the same time."
The DNA strand between the handles contains a special sequence of letters shortly before the end. This so-called termination sequence signals the polymerase to let go of the DNA. The spring can now relax again and pull the handles apart. In this way, the starting sequence of the chain is close to the polymerase, and the molecular replicator can start a new transcription process: and so on. "In this way, our nanomotors can perform pulsating actions," explains Mathias Centola from the research group led by Professor Famulok.
Like other types of motors, this type of motor requires energy. The energy is provided by the "alphabet soup" of transcripts produced by polymerases. Each letter (technical term: nucleotide) has a small tail consisting of three phosphate groups - a triphosphate. In order to attach a new letter to an existing sentence, the polymerase must remove two phosphate groups from it. This releases energy, which is used to connect the letters together. "So our engine uses nucleotide triphosphates as fuel. It can only continue to run when there are sufficient amounts of nucleotide triphosphates."
The researchers were able to show that the motor could be easily combined with other structures. This would make it possible, for example, to wander across surfaces - similar to an inchworm pulling itself along a branch in its own characteristic way. "We also plan to produce a clutch so that we can only use the power of the motor at certain times and leave it idling at other times," Famlock explained. In the long term, motors could become the core of complex nanomachines. However, we still have a lot of work to do before reaching this stage. "
Šulc's laboratory is a highly interdisciplinary laboratory that applies statistical physics and computational modeling methods to a wide range of problems in the fields of chemistry, biology, and nanotechnology. The research group developed new multiscale models to study interactions between biomolecules, particularly in designing and modeling DNA and RNA nanostructures and devices.
"Just as the complex machines we use every day - the chips in airplanes, cars and electronics - require sophisticated computer-aided design tools to ensure they function as intended, the field of molecular science is in desperate need of access to such methods." Professor Tijana Rajh, Dean of the School of Molecular Sciences, said: "Petr Šulc and his research group are conducting highly innovative molecular science research, using methods from computational chemistry and physics to study DNA and RNA molecules in the context of biology and nanotechnology. Our young faculty in the School of Molecular Sciences have achieved extraordinary results, and Professor Šulc is a good example of this."
DNA and RNA are the basic molecules of life. They serve a variety of functions, including information storage and information transfer in living cells. They also have broad application prospects in the field of nanotechnology, where designed DNA and RNA strands can be used to assemble nanoscale structures and devices. It's a bit like playing with Lego, except each Lego brick is only a few nanometers (millionths of a millimeter) in size. Instead of placing each brick where it's supposed to go, you put them in a box and shake them around until only the desired structure comes out.
"There are many promising applications in this area, including diagnostics, therapeutics, molecular robotics and the construction of new materials," Šulc said. "My lab developed the software to design these building blocks, and we work closely with experimental groups at the University of Arizona and other universities in the United States and Europe. As the field continues to advance and we implement new advanced designs and successfully run them at the nanoscale, it is exciting to see our methods being used to design and characterize increasingly complex nanostructures."