Biological engineers have created a programming language that allows them to rapidly and efficiently program and design DNA-encoded circuits, giving new functions to living cells.

MIT biological engineers have developed a programming language – for living cells. Image credit: Janet Iwasa.

There are already a myriad of programming languages. Fortran and C++ allow for rapid computations, PHP is a scripting language for web development, Ruby is a popular object-oriented language – basically whatever people needed to do, they’ve created a programming language for it. But how would you create a programming language for biological cells?

Over the past decade, researchers have built a fair amount of genetic parts that can be programmed, including sensors, networks and even memory switches. But until now, there was no language developed specifically for this.

“It is literally a programming language for bacteria,” says Christopher Voigt, an MIT professor of biological engineering. “You use a text-based language, just like you’re programming a computer. Then you take that text and you compile it and it turns it into a DNA sequence that you put into the cell, and the circuit runs inside the cell.”

The good thing about it is that it’s very simple, without many of the intricacies often encountered in programming.

“You could be completely naive as to how any of it works. That’s what’s really different about this,” Voigt says. “You could be a student in high school and go onto the Web-based server and type out the program you want, and it spits back the DNA sequence.”

The language is based on Verilog, a language used to program electronic component, especially computer chips. To develop the new language, Voigt and his team designed their own computing elements such as logic gates and sensors that can be encoded in a bacterial cell’s DNA. The sensors can detect different substances or compounds, such as oxygen and glucose, as well as physical parameters such as light, temperature and acidity. It’s designed in a way which allows users to add their own sensors.

 “It’s very customizable,” Voigt says.

For now, all these features have been customized for the E. coli bacteria, one of the most common in studies, but researchers are working on expanding the language to other strands of bacteria.

Using this language, they’ve already programmed 60 circuits with different functions, and 45 of them worked correctly the first time they were tested – which is a remarkable achievement. The circuits were also strikingly fast, and the whole process promises to revolutionize DNA engineering. Before, it could take months or years to design such a circuit. Now, it can be done in less than a day.

The team is already looking at some potential applications, including:

• bacteria that can be swallowed to aid in digestion of lactose;
• bacteria that can live on plant roots and produce insecticide if they sense the plant is under attack;
• and yeast that can be engineered to shut off when they are producing too many toxic byproducts in a fermentation reactor.

Journal Reference:

1. A. A. K. Nielsen, B. S. Der, J. Shin, P. Vaidyanathan, V. Paralanov, E. A. Strychalski, D. Ross, D. Densmore, C. A. Voigt. Genetic circuit design automation. Science, 2016; 352 (6281): aac7341 DOI: 10.1126/science.aac7341