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Water quality is assessed by a new DNA computer


Synthetic biologists have created a low-cost, simple-to-use hand-held gadget that can tell consumers whether their water is safe to drink in minutes. The novel gadget performs a variety of logic operations by using powerful and customizable genetic networks that imitate electrical circuits.

Synthetic biologists from Northwestern University have invented a low-cost, simple-to-use hand-held gadget that can tell consumers if their water is safe to drink in seconds.

The novel gadget performs a variety of logic operations by using powerful and customizable genetic networks that imitate electrical circuits.

The researchers designed cell-free molecules into an analog-to-digital converter (ADC), a circuit type used in practically all electronic devices, as one of the DNA-based circuits. The ADC circuit of the water-quality device converts an analog input (contaminants) into a digital output (a visual signal to inform the user).

The findings will be published in the journal Nature Chemical Biology on February 17th.

The gadget, which is made up of eight microscopic test tubes, flashes green when it finds a contamination. The number of tubes that light is determined by the level of pollution. If just one tube illuminates, the water sample is contaminated to a trace level. However, if all eight tubes light up, the water is highly polluted. To put it another way, the greater the contamination level, the stronger the signal.

“We set each tube to have a distinct contamination threshold,” said Julius B. Lucks, the study’s lead author. “The tube with the lowest threshold will remain lit indefinitely. If all of the tubes light up, there is a serious issue. Other sorts of smart diagnostics are now possible because to the development of circuits and programmable DNA computing.”

Lucks is a member of the Center for Synthetic Biology and a professor of chemical and biological engineering at Northwestern University’s McCormick School of Engineering. Jaeyoung Jung, ChloĆ© Archuleta, and Khalid Alam, all of Northwestern, are co-authors on the work.

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Take a look at ROSALIND

The new approach is based on research published by Lucks and his colleagues in Nature Biotechnology in July 2020. The researchers developed ROSALIND (short for “RNA output sensors activated by ligand induction” and named after famous scientist Rosalind Franklin), which could detect 17 distinct pollutants in a single drop of water. When the test discovered a pollutant that exceeded the EPA’s criteria, it either illuminated green or did not, giving a straightforward, easy-to-read positive or negative answer.

Lucks and his colleagues used cell-free synthetic biology to create ROSALIND. Researchers use synthetic biology to pull molecular machinery out of cells, such as DNA, RNA, and proteins, and reprogramme it to do new jobs. Lucks compared ROSALIND’s inner workings to “molecular taste buds” at the time.

“We discovered how bacteria taste things in their water naturally,” he stated. “They do it by using ‘taste buds’ at the molecular level. We can extract those tiny molecular taste buds and place them in a test tube thanks to cell-free synthetic biology. Then we may rewire them to make a visual signal. It glows to make it easy for the user to see if there is a contaminant in the water.”

Molecular intelligence

Lucks and his colleagues have now incorporated a “molecular brain” to the updated version, termed ROSALIND 2.0.

Lucks explained, “The initial platform was a bio-sensor that acted like a taste bud.” “We’ve now incorporated a genetic network that functions similarly to a brain. The bio-sensor detects pollution, but the bio-output sensor’s is sent into the genetic network, or circuit, which performs logic like a brain.”

The reprogrammed “molecular brains” were freeze-dried and placed in test tubes to make them shelf-stable. By adding a drop of water to each tube, a chain of events and interactions is put in motion, resulting in the freeze-dried pellet glowing in the presence of a pollutant.

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Lucks and his colleagues proved that the novel method could detect concentration levels of zinc, an antibiotic, and an industrial metabolite. According to Lucks, providing the level of contamination rather than a simple positive or negative result is critical for informing mitigation strategies.

“People mentioned they needed a platform that could also supply concentration quantities once we debuted ROSALIND,” he added. “Different pollutants at various levels need different approaches. If your water has a low amount of lead, for example, you may be able to handle it by cleansing your water lines before using them. However, if your levels are excessive, you should immediately stop drinking your water and replace your water line.”

Individual empowerment

Lucks and his colleagues anticipate that, in the end, people will be able to test their own water on a regular basis. That might soon be a reality, thanks to low-cost hand-held devices like ROSALIND.

“It’s evident that we need to provide individuals with the knowledge they need to make critical, often lifesaving choices,” Lucks said. “That’s what we’re seeing with COVID-19 at-home tests. People need at-home testing because they want information immediately and on a consistent basis. It’s the same way with water. Water quality must be assessed on a regular basis in a variety of situations. Because contamination levels might alter over time, it’s not a one-time affair.”

The research, titled “Programming cell-free biosensors using DNA strand displacement circuits,” was funded by the US Department of Defense, the National Science Foundation, the Crown Family Center for Jewish and Israel Studies, and The Chicago Community Trust’s Searle Funds.

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