DNA origami folded into tiny motor

The tiny motor could help spark research into future applications such as building molecular factories for useful chemicals or medical probes of molecules inside the bloodstream to detect diseases such as cancer.

“Common macroscopic machines become inefficient at the nanoscale,” said study co-author professor Aleksei Aksimentiev, a professor of physics at the University of Illinois at Urbana-Champagne. “We have to develop new principles and physical mechanisms to realize electromotors at the very, very small scales.”

The experimental work on the tiny motor was conducted by Cees Dekker of the Delft University of Technology and Hendrik Dietz of the Technical University of Munich.

Dietz is a world expert in DNA origami. His lab manipulated DNA molecules to make the tiny motor’s turbine, which consisted of 30 double-stranded DNA helices engineered into an axle and three blades of about 72 base pair length. Decker’s lab work demonstrated that the turbine can indeed rotate by applying an electric field. Aksimentiev’s lab carried out all-atom molecular dynamics simulations on a system of five million atoms to characterize the physical phenomena of how the motor works.

The system was the smallest representation that could yield meaningful results about the experiment; however, “it was one of the largest ever simulated from the DNA origami perspective,” Aksimentiev said.

Mission Impossible to Mission Possible

The Texas Advanced Computing Center (TACC) awarded Aksimentiev a Leadership Resource Allocation to aid his study of mesoscale biological systems on the National Science Foundation (NSF)-funded Frontera, the top academic supercomputer in the U.S.

“Frontera was instrumental in this DNA nanoturbine work,” Aksimentiev said. “We obtained microsecond simulation trajectories in two to three weeks instead of waiting for a year or more on smaller computing systems. The big simulations were done on Frontera using about a quarter of the machine — over 2,000 nodes,” Aksimentiev said. “However, it’s not just the hardware, but also the interaction with TACC staff. It’s extremely important to make the best use of the resources once we have the opportunity.”

Aksimentiev was also awarded supercomputer allocations for this work by the NSF-funded Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) on Expanse of the San Diego Supercomputer Center and Anvil of Purdue University.

“We had up to 100 different nanomotor systems to simulate. We had to run them for different conditions and in a speedy manner, which the ACCESS supercomputers assisted with perfectly,” Aksimentiev said. “Many thanks to the NSF for their support — we would not be able to do the science that we do without these systems.”

DNA as a Building Block

The success with the working DNA nanoturbine builds on a previous study that also used Frontera and ACCESS supercomputers. The study showed that a single DNA helix is the tiniest electromotor that one can build — it can rotate up to a billion revolutions per minute.

DNA has emerged as a building material at the nanoscale, according to Aksimentiev.

“The way DNA base pair is a very powerful programming tool. We can program geometrical, three-dimensional objects from DNA using the Cadnano software just by programming the sequence of letters that make up the rungs of the double helix,” he explained.

Another reason for using DNA as the building block is that it carries a negative charge, an essential characteristic to make the electromotor.

“We wanted to reproduce one of the most spectacular biological machines — ATP synthase, which is driven by electric field. We chose to do our motor with DNA,” Aksimentiev said.

“This new work is the first nanoscale motor where we can control the rotational speed and direction,” he added. It’s done by adjusting the electric field across the solid state nanopore membrane and the salt concentrations of the fluid that surrounds the rotor.

“In the future, we might be able to synthetize a molecule using the new nanoscale electromotor, or we can use it to as an element of a bigger molecular factory, where things are moved around. Or we could imagine it as a vehicle for soft propulsion, where synthetic systems can go into a blood stream and probe molecules or cells one at a time,” Aksimentiev said.

If you think this sounds like something out of a 1960’s sci-fi movie, you are right. In the movie Fantastic Voyage, a team of Americans in a nuclear submarine is shrunk and injected into a scientist’s body to fix a blood clot and need to work quickly before the miniaturization wears off.

As far-fetched as this might sound, Aksimentiev says that the concept and the elements of the machines we are developing today could enable something like this to happen.

“We were able to accomplish this because of supercomputers,” Aksimentiev said. “Supercomputers are becoming more and more indispensable as the complexity of the systems that we build increases. They’re the computational microscopes, which at ultimate resolutions can see the motion of individual atoms and how that is coupled to a bigger system.”

Funding came from ERC Advanced Grant no. 883684 and the NanoFront and BaSyC programmes; ERC Consolidator Grant to H.D. (GA no. 724261), the Deutsche Forschungsgemeinschaft via the Gottfried-Wilhelm-Leibniz Programme (to H.D.) and the SFB863 Project ID 111166240 TPA9; National Science Foundation grant DMR-1827346; the Max Planck School Matter to Life and the MaxSynBio Consortium. Supercomputer time was provided through TACC Leadership Resource Allocation MCB20012 on Frontera and through ACCESS allocation MCA05S028.