Video: This is how the tiny device works. © Mathias Centola, University of Bonn
It snaps open and then contracts again and again: Researchers have created a motor from DNA building blocks that can perform pulsating movements using a sophisticated mechanism. An RNA polymerase pulls a DNA thread between two parts of a V-shaped spring construction and then suddenly lets go of the “pulling rope”. The scientists say that the design could be used in the future as a drive unit for building molecular machines and robots.
Massive constructions can move large and heavy things – but some technical applications also require very small machines and robotic systems. Refining structures has a long tradition. In recent years, however, researchers have ventured into ever more extreme areas: they are now even building machines and robots on a nanoscale. Such tiny things could, among other things, fulfill medical missions in the body, according to the future vision. This topic also forms part of the cover story “The New Robots” in the November 2023 issue of bild der Wissenschaft.
The design of some of these nanomachines uses a technique called DNA origami. The molecular engineers use the nucleotides of the genetic material as building material. Thanks to their special binding activities with one another, these units can be assembled into complex constructions using the process. In this way, structures with specific functional structures and mechanical features can be built. But there is still one aspect of turning them into machines: the development of drive systems has proven to be a major challenge for engineering in the nano world. The international team led by the University of Bonn is now presenting a possible solution to the problem: The researchers have used DNA origami technology to build a nano-motor that could be installed as a drive unit in molecular constructions.
A snapping device made of genetic modules
The structure, which is only around 60 nanometers in size, consists of two elongated components that are connected to a V-shaped structure via a curved connecting element. In the relaxed state, this spring construction assumes a certain, predetermined angle. To put them under tension, the scientists cleverly misused an element of genetics: RNA polymerase. This enzyme attaches to DNA strands and then moves along them using mechanical propulsion. It creates a copy of the DNA using nucleotides from the surrounding medium.
“We have now taken an RNA polymerase and stuck it to one of the two parts of our nano-machine,” explains senior author Michael Famulok from the University of Bonn. “We also stretched a DNA thread between the pieces in the immediate vicinity. The polymerase then grabs this thread to copy it. She pulls him along. The part that has not yet been written off becomes shorter and shorter. This causes the second piece to move closer and closer to the first. In this way, tension builds up in the V-shaped structure,” explains Famulok.
The polymerase pulls on the rope and then lets it go
So that the spring mechanism can suddenly relax, the scientists have built a “release element” into the DNA pull rope: Shortly before the end, it contains a specific sequence of DNA building blocks to which the polymerase reacts: when it encounters these so-called terminations sequence, it detaches itself from the strand. The accumulated tension energy is then suddenly released: the two elongated elements of the spring mechanism snap open. The starting sequence of the thread then comes close to the polymerase again and the tensioning process can begin again. “This means that our nano-motor performs a pulsating movement,” says first author Mathias Centola from the University of Bonn.
The RNA polymerase can do work in the system – but where does the energy come from? As the team explains, it comes from the chemical “alphabet soup” from which the polymerase produces the transcripts: When incorporated, the nucleotides provide the energy for propulsion. This is because each of these molecules has three phosphate groups, two of which the polymerase removes during incorporation. This releases energy, which it uses to link the letter and progress. “So our engine consumes nucleotide triphosphates,” says Famulok.
The team was able to confirm that the whole thing actually works as the theory suggests by observing individual nano-motors using electron microscopy: the snapping movements of the units were clearly visible. The researchers have already shown that the motor can be coupled with other DNA origami structures. There is now potential for drives in the nano world: “In the long term, the motor could become the heart of complex nano-machines. “But there is still a lot of work to be done before then,” concludes Famulok.
Source: University of Bonn, specialist article: Nature Nanotechnology, doi: 10.1038/s41565-023-01516-x