Tuning In: Discovering the ‘Volume Dial’ for Our Body’s Silent Signals

An unconnected electronic device might still operate, yet it produces a significantly better sound when linked to an amplifier and effects. Likewise, environmental toxins and other small molecules present in low amounts within the human body can issue faint signals that remain undetectable without advanced laboratory equipment.

Thanks to an ingenious method in biochemistry that adapts a sensing system already utilized by Northwestern Engineering researchers to assess toxins in drinking water, scientists can now identify and even quantify chemicals at sufficiently low concentrations for practical application outside the laboratory. By incorporating circuitry similar to a volume control to amplify weak signals, the team has paved the way for this system to be used for detecting and monitoring diseases within the human body regarding nucleic acids like DNA and RNA, along with bacteria such as E. coli.

The findings, which detail a system that is tenfold more sensitive than earlier cell-free sensors developed by the team, were published on January 13 in the journal Nature Chemical Biology.

“Biosensors repurposed from natural sources can theoretically detect a wide range of pollutants and indicators of human health, although they typically lack sufficient sensitivity as they stand,” explained corresponding author and Northwestern synthetic biologist Julius Lucks. “By integrating genetic circuitry that performs as an amplifier, we can adjust this biosensing platform to achieve sensitivity standards necessary for applications in environmental and public health monitoring.”

Lucks serves as a professor in chemical and biological engineering at the McCormick School of Engineering and is a co-director of the Center for Synthetic Biology

Engineering a ‘pregnancy test for water’

ROSALIND’s initial model was capable of detecting 17 different contaminants within a single drop of water, illuminating green upon the presence of a contaminant surpassing the standards set by the US Environmental Protection Agency. A subsequent model advanced the platform’s ability to evaluate varying concentrations of contaminants, establishing something more intricate than a “pregnancy test for water.”

Lucks and his associates employed a technique known as cell-free synthetic biology to establish ROSALIND, where molecular machinery—such as DNA, RNA, and proteins—are extracted from cells and then reprogrammed for new functions.

A beneficial bug in the system

Synthetic biologists engaging with DNA and RNA often confront an obstructive adversary called T7 RNA polymerase enzyme, which Lucks likens to the radio battery due to its function in generating output signals. While this enzyme can act as a nuisance within the system by consuming RNA fragments it shouldn’t, causing chaos in nucleic acid circuits, Lucks speculated if it could be harnessed for their benefit.

Lucks references the evolution of the transistor radio to elucidate the enhancements made to the sensing platform developed by his team, known as ROSALIND (named in honor of the renowned chemist Rosalind Franklin and shorthand for “RNA output sensors activated by ligand induction”).

“You could assemble the first transistor radio in your Electronics 101 class, allowing it to receive a radio signal, yet it would have numerous issues,” Lucks noted. “If you move behind a tree, the signal is lost, and moving closer to the source amplifies it. Subsequent iterations of that radio incorporated extra electronic components to correct for and manage these problems. This version essentially adds a volume control to the radio.”

Utilizing a signal amplification technique derived from DNA nanotechnology, which allows a circuit to recycle and replay its input, the researchers discovered a method to enhance the signal of an input molecule. Upon generation of a signal, the “bug” consumes and recycles it, leading to the production of an additional signal. Consequently, the team could identify molecules—like antibiotics and heavy metals—at a fraction of the concentration used by earlier versions.

“We engineered a novel system for amplifying signals in ROSALIND,” asserted first author Jenni Li, a PhD candidate in the Lucks lab. “Thanks to an innovative trick within biochemistry, we can fine-tune the system for identifying compounds at lower concentrations without altering the actual biosensor protein. This entire process is executed within nucleic acid ‘circuits.’ ROSALIND 3.0 is now more sensitive and capable of detecting nucleic acids where it previously could only identify small molecule compounds.”

ROSALIND at work

Prior versions of ROSALIND are currently in use in real-world applications, such as in an ongoing field study in the Chicago region, monitoring lead in drinking water. According to Lucks, the novel aspects of the team’s “3.0” model can be seamlessly integrated into this and various other endeavors.

“We are additionally refining ROSALIND to recognize human health indicators, food safety markers, and agricultural substances, thereby expanding the potential applications of this platform technology,” Lucks remarked. “This new sensitization method is versatile, indicating that we will be able to develop sensors capable of detecting compounds at actionable levels more swiftly in the future.”