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Detect water pollution: DNA computer could tell you if your drinking water is contaminated

Detect water pollution: DNA computer could tell you if your drinking water is contaminated

A simple water pollution test involving modified DNA strands can signal contamination levels, and this biological system can perform logical operations like those performed by computers.

Technology


February 17, 2022

The DNA Computer – although not set up for formal analysis

Julius Lucks/Northwestern University

A DNA-controlled biological computer offers a simple and inexpensive way to test the concentration of contaminants in drinking water. And experiments show that logical operations borrowed from computing can be embedded in DNA to make future biological computers much more powerful at detecting contaminants.

Julius Chances at Northwestern University in Illinois and his colleagues in 2020 created a biosensor capable of detecting contaminants in a single drop of water. It contains proteins that react to the presence of certain chemicals by producing fluorescent molecules. This easily spotted reaction acts as a warning that a water sample is polluted with these chemicals.

The reactions involved were inspired by mechanisms that evolved naturally within bacteria. Lucks says scientists first tried to engineer the bacteria to perform the tests, but it was a challenge to keep them alive and prevent them from spreading through the environment. This led to the search for a cell-free synthetic biological version, where protein-based mechanisms are removed from bacteria and used in isolation.

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“In synthetic biology, we’re trying to reuse these molecular machines that sense toxins and redesign them to work the way we want them to, maybe rewire them to do different things,” Lucks says. “You don’t really want to release an artificial microbe into the water that you’re trying to measure the quality of.”

Now the team has created a more advanced version of the system that can not only warn of the presence of dangerous chemicals, but also flag the quantities present so that proportionate action can be taken.

The system, dubbed ROSALIND 2.0, features eight small test tubes, each containing a biosensor with different sensitivity to contaminants. If only one tube glows, the water sample has only traces of contamination. But as more and more tubes shine, the water turns out to be more and more polluted.

Lucks says the test works by using “decoy” DNA strands. These are designed to bind strongly to a key intermediate in the reaction with the contaminant, preventing the production of the final fluorescent product.

Each tube contains progressively larger amounts of this DNA. Since the final fluorescent step of the reaction does not occur until after decoy DNA has been exhausted, this means that a tube with a low amount of decoy DNA may fluoresce in the presence of the contaminant, but a tube with a large amount of this DNA may not . It is possible to measure the contaminant level simply by looking at where along the row of eight tubes the fluorescent reaction stops.

Lucks and his team demonstrated that ROSALIND 2.0 could successfully detect zinc, an antibiotic and an industrial metabolite.

Cell-free tests can also be freeze-dried for easy storage and transport, then activated when needed simply by dropping a water sample into each test tube.

Establishing the concentration of a contaminant helps decide what corrective action is needed. If you have small amounts of lead in your drinking water supply, for example, you may only need to flush the water lines before using them. But if you have high levels, you may need to stop drinking water immediately.

“Everyone should have these things,” Lucks says. “You need to know that your water is safe to drink.”

Since existing technology for assessing water quality can be expensive, he hopes ROSALIND 2.0 can help. “We’re trying to do the simplest, most robust thing you can imagine, so it’s hopefully foolproof,” he says.

Lucks and his team have also demonstrated that modified DNA can be used to perform logical operations, such as those of computers. Not only can it be made to react to the presence of a material, like in ROSALIND 2.0, but they think it can only be made to react when two specific chemicals are found, or when none are found. This paves the way for much more sophisticated analysis to be incorporated into equally robust and easy-to-use tests.

Journal reference: Nature Chemistry Biology, DOI: 10.1038/s41589-021-00962-9

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