New programming language helps hack living cells
The biological engineers at MIT have developed a programming language which enables them to interact with living cells. As part of their research, the researchers have already programmed 60 DNA circuits with several functions.
MIT biological engineers have created a programming language which allows them to design DNA-encoded circuits that give living cells new functions. The system could eventually be used to code a program for any function.
Christopher Voigt, an MIT professor of biological engineering dubbed the system “a programming language for bacteria” and explained that hacking living cells is no different than programming a computer since they both use a text-based language. Dr. Voigt added that the text is then compiled and turned into a DNA sequence “that you put into the cell, and the circuit runs inside the cell.” The MIT professor along with colleagues at Boston University and the U.S. National Institute of Standards and Technology have used this new programming language to create circuits which can detect up to three inputs and respond differently. Their experiment is described in the April 1 issue of Science.
This new programming language could be used in the future to create bacterial cells which can produce a cancer drug when they encounter a tumor or create yeast cells which can stop their own fermentation process if there are too many toxic byproducts. The researchers intend to make the user design interface available on the Web.
Anyone can use this programming language to hack living cells
One of the immediate perks of this new programming language is that users do not need special knowledge of genetic engineering. Until now, designing DNA circuits has been a tough process which required great expertise. Plus, people had to know everything there is to know about these circuits before designing them.
Dr. Voigt noted that people who use this programming language can be “completely naive as to how any of it works.” This language is based on Verilog, widely used to program computer chips. To come up with a version of the language which would work for cells, the researchers created computing elements such as sensors and logic gates which can be encoded in the DNA of a bacterial life. Although the sensors can recognize different compounds and environmental conditions, they are also “very customizable.”
Benefits and challenges
The team’s greatest challenge was creating the 14 logic gates used in the circuits so that they would not meddle with each other once put in a living cell’s environment. These genetic parts are currently optimized for E.coli. However, the team of researchers is trying to expand the language for other strains of bacteria. The purpose is to allow users to write one program and compile it for distinct organisms to get the correct DNA sequence for each one.
With the help of this programming language, the researchers have already programmed 60 circuits with different functions. According to the announcement, 45 of them worked correctly the first time they were tested. One of the circuits programmed by the researchers is the biggest biological circuit ever built and contains seven logic gates, as well as roughly 12,000 base pairs of DNA.
Dr. Voigt added that one of the most important advantages of this technique is speed. Building these types of circuits would have taken years in the past, but “now you just hit the button and immediately get a DNA sequence to test.” The team is currently working on a few different applications using this approach: bacteria which can live on plant roots and produce insecticide if the plant is under attack, bacteria which can be swallowed to help digest lactose and yeast which can be used to shut off when too many toxic byproducts are produced in a fermentation reaction.