Fluorescent RNA sensor gets 10 times more sensitive for water safety

Water is largely tasteless to humans. But to the microbial world, it is anything but. Bacteria that live in contaminated environments have spent millions of years evolving exquisitely sensitive molecular detectors—proteins that latch onto specific chemical threats and trigger a cellular response.

Borrowing nature’s pollution detectors

Julius Lucks, a chemical and biological engineer at Northwestern University, is asking a deceptively simple question: what if we could borrow those detectors, strip them out of the cell entirely, and put them to work for us?

The answer is ROSALIND—a platform named after chemist Rosalind Franklin, and short for RNA Output Sensors Activated by Ligand Induction.

Rather than building sensors from scratch, Lucks and his team reverse-engineer the sensing molecules that microbes already use to detect contaminants, then reprogram them inside a cell-free system: a carefully prepared mixture of molecular machinery—DNA, RNA, and proteins—that can run biological reactions outside of any living organism.

When ROSALIND detects a target chemical, it triggers the production of a fluorescent RNA molecule. The sample glows. Minimal laboratory equipment required. No microbiologist needed on site.

Turning up the signal’s volume

The earliest version of the platform could screen for 17 different contaminants from a single drop of water, flagging anything that exceeded EPA safety thresholds. But sensitivity was a limiting factor—some contaminants lurk at concentrations so low that even a well-designed biosensor might miss them.

Lucks’s team published a solution in Nature Chemical Biology, a signal amplification circuit that exploits an enzyme—one that had long been considered an annoyance by RNA engineers—to recycle and replay detection signals, effectively turning up the volume on weak readings.

The latest iteration of ROSALIND is now 10 times more sensitive than its predecessor, and for the first time can detect nucleic acid targets like DNA fragments and RNA, not just small molecules and metals.

From lab bench to real communities

The real test, though, isn’t in the lab. ROSALIND is already in the field. In the Chicago area, households are using the platform to test their tap water for lead.

In rural Kenya, Lucks’s team has conducted field trials in dozens of households measuring fluoride levels in drinking water—a serious public health concern in parts of East Africa where geologic sources naturally elevate concentrations far beyond safe limits. Field trials of a CRISPR-based crop pathogen detector developed in his lab are underway in Kenya and Uganda.

“Taking the technology out of the lab and into the field is critical—not only for discovering and correcting failure modes in the tech, but for interfacing with the stakeholders you are trying to help with the tech,” said Lucks. “Partnering with social scientists in this work has changed our perspective to think about co-developing this technology with the people that need it the most.”

Who’s behind this story?

Sadie Harley

BSc Life Sciences & Ecology. Microbiology lab background with pharmaceutical news experience in oil, gas, and renewable industries.

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Robert Egan

Bachelor’s in mathematical biology, Master’s in creative writing. Well-traveled with unique perspectives on science and language.

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