Scientists have modified a sensing platform to identify and quantify chemicals at much lower concentrations, making it useful beyond laboratory settings. This new system is ten times more sensitive than earlier models developed by the team, paving the way for its application in disease detection and monitoring of nucleic acids and bacteria in the human body.
Just as an electric instrument sounds far better when connected to an amplifier, toxins and other tiny molecules at low concentrations in our environment or body may give off faint signals that require specialized laboratory technology to detect.
Thanks to an innovative biochemical technique, researchers have adapted a sensing platform that the team at Northwestern University originally used for measuring toxins in drinking water. This enhanced system can now identify and measure chemicals at concentrations suitable for real-world applications. By incorporating circuitry similar to a volume knob to amplify weak signals, the team has made it possible to use this technology for detecting diseases and monitoring nucleic acids like DNA and RNA, as well as bacteria like E. coli.
The findings, indicating a system that is ten times more sensitive than earlier cell-free sensors from the team, were published today (Jan. 13) in the journal Nature Chemical Biology.
“Nature-derived biosensors can theoretically identify a wide range of contaminants and health indicators, but they often lack sufficient sensitivity,” stated Julius Lucks, a synthetic biologist at Northwestern and the study’s lead author. “By introducing genetic circuitry that functions like an amplifier, we elevate this biosensing platform to meet the sensitivity standards necessary for environmental and health monitoring.”
Lucks holds a professorship in chemical and biological engineering at Northwestern’s McCormick School of Engineering and co-directs the Center for Synthetic Biology.
Creating a ‘pregnancy test for water’
The initial version of ROSALIND could detect 17 different contaminants in a single water drop, illuminating in green when specific contaminants surpassed the U.S. EPA standards. A subsequent iteration allowed the platform to assess varying contaminant concentrations, making it a more advanced tool than a simple “pregnancy test for water.”
Lucks and his team utilized cell-free synthetic biology techniques to create ROSALIND, removing molecular machinery—like DNA, RNA, and proteins—from cells for reprogramming to perform new tasks.
A beneficial glitch in the system
While working with DNA and RNA, synthetic biologists frequently encounter an unwanted element known as the T7 RNA polymerase enzyme. Lucks likens its function to a radio’s battery for generating output signals. However, this enzyme can also disrupt results by destroying unwanted RNA fragments and causing issues within nucleic acid circuits. Lucks speculated that this enzyme could be harnessed effectively instead.
To illustrate improvements in their sensing platform, Lucks referred to the evolution of the transistor radio, which is named ROSALIND (in honor of esteemed chemist Rosalind Franklin and short for “RNA output sensors activated by ligand induction”).
“In your Electronics 101 course, you might build a basic transistor radio—one that can receive a signal but has many problems,” Lucks explained. “When you move behind an obstruction, the signal fades, and it gets stronger as you approach the source. Subsequent radio models incorporated additional circuitry to mitigate these issues. Our latest iteration adds a volume control ‘knob’ to the radio.”
Employing a signal enhancement technique rooted in DNA nanotechnology, the researchers discovered a way to amplify the input signals. The “bug” consumes and recycles the generated signal, thus creating another one. This innovation enabled the team to recognize molecules like antibiotics and heavy metals at significantly lower concentrations than previous versions.
“We developed a new method for amplifying signals in ROSALIND,” noted Jenni Li, the first author and a Ph.D. candidate in the Lucks lab. “Using a clever biochemical strategy allows us to refine the system for detecting lower-level compounds without altering the biosensor protein itself, all facilitated through nucleic acid ‘circuits.’ ROSALIND 3.0 is now more adept at detecting nucleic acids alongside previously detectable small molecules.”
ROSALIND in action
Earlier versions of ROSALIND are already being used in practical applications, such as a current field study in the Chicago area, where they are detecting lead in drinking water. According to Lucks, the enhancements included in their “3.0” model can be seamlessly integrated into ongoing projects.
“We are also refining ROSALIND to identify human health indicators, food safety markers, and agricultural compounds, broadening the applications of this technology,” Lucks mentioned. “This new amplification technique is adaptable, enabling faster development of sensors for detecting actionable compound levels in the future.”
Funding for this research was provided by the National Institutes of Health training grant (T32GM008449) via Northwestern’s Biotechnology Training Program, the National Science Foundation Synthesizing Biology Across Scales training initiative (2021900), and Northwestern’s Graduate School Cluster in Biotechnology, System, and Synthetic Biology. Additional support was received from Army Contracting Command (W52P1J-21-9-3023), the Defense Advanced Research Projects Agency (DARPA) (N660012324041), and the National Science Foundation (2310382).
The ROSALIND technology is being commercialized by Northwestern startup Stemloop. Lucks has vested interests in and affiliations with Stemloop. Northwestern also holds financial interests (equity, royalties) in Stemloop.
