Once the technology is fully developed, tiny biological computers composed of DNA may transform the way we identify and treat a variety of diseases. The limited lifespan of these DNA-based devices, which can function in both cells and liquid solutions, has proven to be a significant obstacle.
The PCs are exhausted after just one use. Now, scientists at the National Institute of Standards and Technology (NIST) may have created durable biological computers that might survive inside cells.
The authors of an article in the journal Science Advances choose to create computers using RNA rather than the more conventional DNA-based method. The findings show that RNA circuits are just as reliable and adaptable as their DNA-based equivalents.
Furthermore, RNA is a good choice for strong, durable biological computers because living cells may be able to continuously build these RNA circuits, which is not always possible with DNA circuits. Biological computers can be taught to perform a variety of activities, just like the computer or smart device you are probably using to read this.
“The difference is, instead of coding with ones and zeroes, you write strings of A, T, C, and G, which are the four chemical bases that make up DNA,” said Samuel Schaffter, NIST postdoctoral researcher and lead author of the study.
Researchers can control what a strand of nucleic acid binds to by constructing a certain sequence of bases into it. A strand may be designed to bind to particular regions of DNA, RNA, or proteins linked to disease; this attachment may then set off chemical processes involving other strands in the same circuit, which process chemical information and eventually result in a useful output.
Depending on the output, a medicine could be used to treat a condition or a detectable signal to help with medical diagnosis.
However, DNA is a weak substance that can easily disintegrate under certain circumstances. Since they frequently contain proteins that break down nucleic acids, cells can be hostile environments. Furthermore, even if DNA sequences survive long enough to find their intended target, the chemical connections they create subsequently render them ineffective.
For me, these needed to work in a test tube as predictively as DNA computing. The nice thing with DNA circuits is most of the time, you can just write out a sequence on a piece of paper, and it’ll work the way you want. The key thing here is that we did find the RNA circuits were very predictable and programmable, much more so than I thought they would be, actually.Samuel Schaffter
“They can’t do things like continuously monitor patterns in gene expression. They are one use, which means they just give you a snapshot,” Schaffter said.
RNA shares many of DNA’s problems with being a biological computer building block because it is also a nucleic acid. It can degrade quickly, and once a strand chemically bonds to a target molecule, it is no longer functional.
But unlike DNA, under the appropriate circumstances, RNA might be a renewable resource. Schaffter and his colleagues had to first demonstrate that RNA circuits, which cells should theoretically be able to make, could function just as effectively as the DNA-based kind in order to take use of that advantage.
The advantage of RNA over DNA comes from a naturally occurring physiological process called transcription, in which proteins continuously create RNA using a cell’s DNA as a template. A cell would continuously create the computer components if the DNA in its genome contained the instructions for a biological computer’s circuitry.
Single strands of nucleic acids in a circuit can easily wind up bound to other strands in the same circuit during the biological computing process. This undesirable consequence inhibits circuit components from binding to their intended destinations. Because of the way these circuits are designed, various components frequently fit together naturally.
DNA sequences that makeup strand displacement circuits in computers are often generated separately and in a double-stranded form (in machines rather than cells) to prevent unwanted binding.
This double strand behaves as a locked gate that would only open if the target sequence appeared and replaced one of the strands since every chemical base on either strand is connected to a base on the other.
Schaffter and Elizabeth Strychalski, a co-author of the paper and leader of NIST’s Cellular Engineering Group, attempted to replicate this “locked gate” function in their RNA circuit while keeping in mind that cells would eventually need to make these locked gates on their own.
The sequences were created so that one-half of the strands may join flush with the other half in order to give cells the best possible chance of success. If RNA sequences were to bind in this manner, they would fold in on themselves like a hotdog bun, ensuring that they are locked.
However, for the gates to function correctly, they would need to be made of two chemically bound yet separate strands, more akin to a hamburger bun or sandwich than a hotdog bun. By encoding a section of RNA known as a ribozyme close to the gates’ folding point, the team was able to create the double-stranded structure in its gates.
This specific ribozyme, which was extracted from the hepatitis virus genome, would split into two different strands when the RNA strand it was buried in folded. The authors examined whether their circuits could carry out simple logical processes, such as unlocking their gates only in certain circumstances, such as when one of two particular RNA sequences was present or only when both were.
Additionally, they constructed and tested circuits composed of several gates that carried out various logical processes sequentially. These circuits wouldn’t start to unlock their gates one at a time like dominoes unless they ran into the correct mix of sequences.
In the trials, several circuits were exposed to fragments of RNA, some of which the circuits were built to attach to, and their output was then measured. In this instance, a fluorescent reporter molecule served as the output at the conclusion of each circuit and lit up when the last gate was released.
As the circuits analyzed inputs, the researchers also monitored the rate at which the gates unlocked and compared their findings to those of computer models.
“For me, these needed to work in a test tube as predictively as DNA computing. The nice thing with DNA circuits is most of the time, you can just write out a sequence on a piece of paper, and it’ll work the way you want,” Schaffter said. “The key thing here is that we did find the RNA circuits were very predictable and programmable, much more so than I thought they would be, actually.”
Since RNA can be transcribed to replace a circuit’s components, the similarity in performance between DNA and RNA circuits may suggest that switching to the latter is advantageous.
And other DNA circuits that scientists have already created to carry out different jobs could conceivably be replaced with RNA equivalents and behave in the same manner. The study’s scientists must advance the technology farther, though, in order to be certain.
The authors of this study showed that transcribable circuits are functional, but they have not yet created any of them using the actual cellular transcription machinery. Instead, using a method identical to that used to create DNA for scientific research, machines manufactured the nucleic acids. In order to proceed, DNA must be inserted into an organism’s genome, where it will act as a design template for RNA circuit parts.
“We’re interested in putting these in bacteria next. We want to know: Can we package circuit designs into genetic material using our strategy? Can we get the same sort of performance and behavior when the circuits are inside cells?” Schaffter said. “We have the potential to.”