Once the technology is fully developed, tiny biological computers comprised of DNA could transform the way we diagnose and treat a variety of ailments. However, the fact that these DNA-based devices can operate in both cells and liquid solutions has proven to be a huge stumbling block. The PCs are exhausted after just one use.
Researchers at the National Institute of Standards and Technology (NIST) believe they have created long-lasting biological computers that might survive inside cells.
The authors of a work published in Science Advances forego the usual DNA-based approach in favor of using the nucleic acid RNA to construct computers. The findings show that RNA circuits are just as reliable and adaptable as their DNA-based counterparts.
Furthermore, unlike DNA circuits, living cells may be able to generate these RNA circuits on a continuous basis, indicating that RNA is a good choice for strong, long-lasting biological computers.
Biological computers, like the computer or smart gadget you’re reading this on, may be trained to perform a variety of activities.
“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 precise sequence of bases into it. A strand might be designed to latch to specific portions of DNA, RNA, or proteins linked to an illness, then initiate chemical interactions with other strands in the circuit to analyze chemical data and eventually provide some sort of useful output.
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.
Samuel Schaffter
That output could be a detectable signal that aids medical diagnosis or a therapeutic medication that treats an illness.
However, DNA is not the most durable substance and can easily break down under certain circumstances. Because cells generally contain proteins that break up nucleic acids, they might be unfriendly settings. Even if DNA sequences survive long enough to recognize their target, the chemical interactions that occur later render them worthless.
“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.
Because it is a nucleic acid, RNA has many of the same problems as DNA when it comes to being a biological computer building block. It degrades quickly, and once a strand chemically bonds to a target molecule, it is no longer functional.
However, unlike DNA, RNA may be a renewable resource under the correct circumstances. To take advantage of this advantage, Schaffter and his colleagues had to show that RNA circuits, which cells might theoretically make, could perform equally as well as DNA circuits.
The advantage of RNA over DNA comes from transcription, a natural biological process in which proteins make RNA on a continual basis utilizing a cell’s DNA as a template. If the DNA in a cell’s genome coded for the circuit components in a biological computer, the cell would continually create those components.
Single strands of nucleic acids in a circuit can readily become bound to other strands in the same circuit during the biological computing process, causing circuit components to fail to bind to their intended destinations. Different components will often be natural fits for each other due to the design of these circuits.
To avoid unwanted binding, it normally manufactured independently DNA sequences used in computers known as strand displacement circuits and in a double-stranded form (in machines rather than cells).
This double strand functions as a locked gate, with each chemical base on one strand connected to a base on the other. It would only unlock if the target sequence came along and replaced one of the strands.
Schaffter and Elizabeth Strychalski, the study’s co-author and the leader of NIST’s Cellular Engineering Group, attempted to replicate this “locked gate” function in their RNA circuit, keeping in mind that cells would eventually have to create these locked gates themselves.
The researchers constructed the sequences so that one-half of the strands could join flush with the other half, setting the cells up for success. When RNA sequences bind in this fashion, they fold in on themselves like a hotdog bun, guaranteeing that they are locked in place.
However, the gates would need to be two chemically bound yet different strands, similar to a hamburger or sandwich bun rather than a hotdog bun, to work correctly. The double-stranded design in the gates was achieved by coding a length of RNA called a ribozyme near the gates’ folding point.
After the RNA strand it was contained in folded, this ribozyme from the genome of a hepatitis virus would break itself, forming two distinct strands.
The researchers examined if their circuits could execute simple logical processes such as only unlocking their gates in specific conditions, such as when one of two specific RNA sequences was present or only when both were present at the same moment.
They also constructed and tested circuits made up of many gates that performed various logical functions in sequence. These circuits’ gates would only unlock one by one like dominoes when they encountered the correct combination of sequences.
The studies entailed exposing various circuits to RNA fragments, some of which the circuits were designed to attach to, and monitoring the circuits’ output. The fluorescent reporter molecule that would light up after the final gate was opened was the output at the conclusion of each circuit in this scenario.
The researchers also measured how quickly the gates unlocked as the circuits processed inputs and compared their findings to computer model projections.
“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.”
Because RNA can be transcribed to replace a circuit’s components, the equivalent performance of DNA and RNA circuits may indicate that switching to the latter may be good.
Many existing DNA circuits built by researchers to do various functions may conceivably be replaced by RNA counterparts and behave the same way. To be sure, the study’s authors need to push the technology even further.
The scientists demonstrated that transcribable circuits operate in this investigation, although they have not yet created them using real cellular transcription machinery.
Instead, machines used a procedure similar to that used to make DNA for study to synthesis the nucleic acids. Inserting DNA into an organism’s genome, where it will serve as a template for RNA circuit components would be the next stage.
“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.”
