A programming language for building synthetic DNA

Similar to how computer scientists use the Java and Python programming languages ​​to write computer code, chemists will soon be able to use a defined set of instructions to "program" the behavior of DNA molecules inside a test tube or cell.

A research team from the University of Washington has succeeded in developing a programming language for chemists that will allow them to accelerate the development of a network that can direct the behavior of chemical reactions in the same way that electronic controllers direct the activity of cars, robots and other devices. In the field of medicine, such networks could be used as sophisticated systems for drug delivery or as sensors for detecting diseases at the cellular level. The research findings were published in the scientific journal Nature Nanotechnology.

Chemists and chemistry lecturers use grids to demonstrate chemical reactions, grids based on a century-old language of equations that describe how mixtures of chemicals behave. Engineers at the University of Washington are taking this language one step further and using it to write software that directs the movement of molecules designed on demand.

"We started with an abstract, mathematical description of a chemical system, and then used DNA to build molecules that illustrate the desired dynamics," said Georg Seelig, a University of Washington professor of electrical engineering and computer science. "Our vision is that eventually it will be possible to use this technology to build tools for general purposes."

Today, when a biologist or chemist creates a certain type of molecular network, the engineering process is complex, cumbersome and unique to that system only. The engineers from the University of Washington wanted to create an infrastructure that would provide scientists with greater flexibility. The lead researcher compares their new approach to programming languages ​​that teach a computer what to do. "I think our method is very attractive because it allows you to solve more than just one problem," notes the lead researcher. "If you want the computer to perform a different action, you simply program the instruction for it. Our project is very similar to this - we can tell chemistry what to do."

Humans and other species already have complex networks of nanometer-sized molecules that help regulate cell activity and maintain the normal functioning of the body. Scientists today are looking for new ways to develop synthetic systems that behave like biological systems in the hope that these synthetic molecules can help the body's normal functions. To this end, there is a need to develop synthetic DNA molecules that change according to their defined function.

Although the new method is not yet ready for application in the field of medicine, future use of it will be able to utilize these networks to create molecules that undergo self-assembly inside the cells and that can be used as "smart" sensors. These molecules can be assimilated into the cells, and then programmed to detect defects in the cell and respond to it as required, possibly, for example, by directly delivering drugs to those cells.
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