An illustration of DNA
A type of DNA computer that shows results through the motion of tiny beads could massively increase the parallel processing power of such machines.
DNA computers take up less space than silicon-based ones and can work in wet environments. They could be used for applications such as detecting contamination in drinking water or monitoring sugar levels in the body.
Previous designs have used fluorescent labels to show results and can only output tens of results simultaneously. They also require complex microscopes to read these findings.
“One hundred-fold is a conservative estimate of how much more parallel processing we can do with our DNA computer compared to ones that use fluorescent labels,” says Khalid Salaita at Emory University in Atlanta, Georgia.
Salaita and his colleagues made the computers out of DNA-coated glass microbeads that either roll or stall on the surface of a gold chip depending on how the DNA strands interact with molecules attached to the chip’s surface. Rolling is equivalent to an output of 1, while stalling corresponds to an output of 0.
The results of the computation can be detected by tracking the motion of the beads using a smartphone camera with a simple magnifying glass attached to it.
“That’s the wild thing. You can convert the information from the DNA computational operation to the macroscopic world using a standard smartphone in just 15 minutes,” says Salaita.
The team engineered “guide” DNA molecules onto the beads, which can bind to matching RNA molecules that are attached to the chip surface. When this occurs, the beads stay still, but when an enzyme called RNaseH is added to the chip, this enables the beads to roll by breaking the DNA-RNA complexes.
The researchers then added a DNA “lock complex” into the computer, which enabled the presence or absence of a specific DNA molecule to control the movement of the bead. They confirmed that the presence of the DNA molecule stalled the bead, while its absence allowed the bead to roll. This system can be easily adapted to detect any DNA of interest in the environment.
As there are thousands of possible microbeads with different shapes and sizes, the researchers say the computers could output thousands of read-outs in parallel. They hope the device could provide a quick way to detect virus levels in saliva. “The really neat thing is that multiple parallel operations could be used to figure out if you have SARS-CoV-2, but also if you have influenza A and another pathogen, for example,” says Salaita.
However, further work is needed to find ways to restock the RNA molecules on the chip surface, which can degrade after 24 hours and limit the lifespan of the computers.