Genetic networks mimic electronic circuits

Test tubes containing water samples glow green inside an illuminator, indicating contamination. Credit: Northwestern University

Genetic networks mimic electronic circuits to perform a range of logical functions.

Equipped with a series of eight small test tubes, the device lights up green when it detects a contaminant. The number of tubes that glow depends on the amount of contamination present. If only one tube glows, the water sample shows evidence of contamination. But if all eight tubes glow, then the water is seriously contaminated. In other words, the higher concentration of contamination leads to a higher signal.

“We programmed each tube to have a different contamination threshold,” said Julius B. Lucks of the McCormick School of Engineering, who led the research. “The tube with the lowest threshold will light up all the time. If all the tubes light up, there is a big problem. Building and programmable circuits[{” attribute=””>DNA computing opens up many possibilities for other types of smart diagnostics.”

Lucks is a professor of chemical and biological engineering at Nothwestern Engineering and a member of the Center for Synthetic Biology. The paper’s co-authors include Jaeyoung Jung, Chloé Archuleta, and Khalid Alam — all from Northwestern.

DNA Computer Water Quality

Testing water from an area affected by wildfires in California. Credit: Northwestern University

Meet ROSALIND

The new system builds off work that Lucks and his team published in Nature Biotechnology in July 2020. In that work, the team introduced ROSALIND (named after famed chemist Rosalind Franklin and short for “RNA output sensors activated by ligand induction”), which could sense 17 different contaminants in a single drop of water. When the test detected a contaminant exceeding the US Environmental Protection Agency’s standards, it either glowed green or not to give a simple, easy-to-read positive or negative result.

To develop ROSALIND, Lucks and his team employed cell-free synthetic biology. With synthetic biology, researchers take molecular machinery — including DNA, RNA, and proteins — out of cells, and then reprogram that machinery to perform new tasks. At the time, Lucks likened ROSALIND’s inner workings to “molecular taste buds.”

“We discovered how bacteria naturally taste things in their water,” he said. “They do it with little ‘taste buds’ at the molecular level. Cell-free synthetic biology allows us to remove these small molecular taste buds and put them in a test tube. We can then “rewire” them to produce a visual signal. It glows to allow the user to quickly and easily see if there is a contaminant in the water.

Molecular intelligence

Now, in the new version – dubbed ROSALIND 2.0 – Lucks and his team have added a “molecular brain”.

“The initial platform was a bio-sensor, which acted like a taste bud,” Lucks said. “Now we’ve added a genetic network that works like a brain. The biosensor detects contamination, but then the output of the biosensor feeds the genetic network, or circuitry, which functions like a brain to perform logic.

There are many cases where water quality should be measured regularly. It’s not a one-time thing, as contamination levels can change over time. — Julius Lucks, Professor of Chemical and Biological Engineering

The researchers freeze-dried the reprogrammed “molecular brains” to become shelf-stable and put them in test tubes. Adding a drop of water to each tube triggers a web of reactions and interactions, ultimately causing the freeze-dried tablet to glow in the presence of a contaminant.

To test the new system, Lucks and his team demonstrated that it could successfully detect concentration levels of zinc, an antibiotic, and an industrial metabolite. Giving the level of contamination — rather than just a positive or negative result — is important to inform mitigation strategies, Lucks said.

“After introducing ROSALIND, people said they wanted a platform that could also give amounts of focus,” he said. “Different contaminants at different levels require different strategies. If you have a low level of lead in your water, for example, you may be able to tolerate it by flushing your water pipes before using them. But if you have high levels, you should stop drinking your water immediately and replace your water line.

Empower individuals

Ultimately, Lucks and his team hope to empower individuals to regularly test their own water. With inexpensive portable devices like ROSALIND, this could soon become a reality.

“Clearly we need to empower people with information to make important, sometimes life-saving decisions,” Lucks said. “We are seeing this with home testing for COVID-19[female[feminine. People need home tests because they need this information quickly and regularly. It’s the same with water. There are many cases where water quality should be measured regularly. This is not a one-time thing as contamination levels can change over time.

Reference: “Programming Cell-free Biosensors with DNA Strand Displacement Circuits” by Jaeyoung K. Jung, Chloé M. Archuleta, Khalid K. Alam and Julius B. Lucks, February 17, 2022, Nature Chemistry Biology.
DOI: 10.1038/s41589-021-00962-9

The study was supported by the US Department of Defense, the National Science Foundation, the Crown Family Center for Jewish and Israel Studies and the Searle Funds of the Chicago Community Trust.

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