Biological circuits, made of synthetic DNA, have incredibly vast and important medical applications. Even though this technology is still early-stage, the approach has been used to create tests for diagnosing cancer and identifying internal injuries, such as traumatic brain injury, hemorrhagic shock, and more. As well, synthetic biological circuits can be used to precisely deliver drugs into cells, at specific doses as needed.
The number of possible applications of biological circuits is vast, as too are the calculations required to identify the appropriate chemical reactions for them. But designing these circuits will now be easier, thanks to a newly improved upon software program. The advancement is described in a recent study published in IEEE Design & Test.
Renan Marks, an Adjunct Professor of the Faculty of Computing at the Universida de Federal de Mato Grosso do Sul (UFMS), was involved in the study. His team initially created a software program called DNAr, which researchers can use to simulate various chemical reactions and subsequently design new biological circuits. In their most recent work, they developed a software extension for the program, called DNAr-Logic, that allows scientists to describe their desired circuits at a high-level. The software takes this high-level description of a logical circuit and converts it to chemical reaction networks that can be synthesized in DNA strands.
Marks says an advantage of his team’s new software extension is that it will allow scientists to focus more on designing the circuits, rather than worry about the calculations and details of the chemical chain reactions. “They can design and simulate [biological circuits] using DNAr-Logic without previous knowledge in chemistry and without writing hundreds of reactions—and differential equations needed to simulate its dynamic behavior—by hand,” says Marks. “The software lifts the burden of chemical reactions details from the scientist's shoulders.”
His team tested the new software in a series of simulations. “The results revealed that logic circuits could be flawlessly designed, simulated, and tested,” says Marks, noting that they were able to use DNAr-Logic to design some synthetic biological circuits capable of generating up to 600 different reactions.
However, there are still a number of barriers in fully realizing this technology in medical applications. One outstanding issue is that biological circuits made up of loose strands of DNA may undergo “leak reactions.” This is when some strands might inadvertently react with other strands in the solution, resulting is an incorrect “computation.” Marks acknowledges that, while issues such as leak reactions still need to be addressed, synthetic biological circuits have an immense amount of potential. “This new field of research opens endless possibilities,” he says.
Moving forward, Marks says, “I plan to continue developing new extensions to expand the DNAr software with new capabilities which other researchers could rely upon. Also, I plan to use DNAr as a framework to assist in researching and developing new circuits based on algorithms that can help health professionals diagnose illnesses faster and be more effective in health treatments.”
This article appears in the August 2021 print issue as “Building DNA Logic.”