Near-IR Biosensors Use DNA Anchors to Target Range of Molecules

To build a flexible sensor for optically detecting a range of viruses and bacteria, a group of researchers from Ruhr University Bochum (RUB), the Fraunhofer Institute for Microelectronic Circuits and Systems (IMS), and ETH Zurich used semiconducting, single-walled, fluorescent carbon nanotubes. The modular sensors, with fluorescence in the near-infrared (NIR), are based on DNA anchors that act as molecular handles.

Carbon nanotubes can be noncovalently modified to create sensors that change their fluorescence when interacting with biomolecules. However, noncovalent chemistry hinders the sensors’ ability to recognize molecules consistently and perform reliable signal transduction.

A 3D-printed model of a carbon nanotube, the main building block for the new biosensors. Unlike this 3D-printed model, the nanotubes that are used for the biosensors are 100,000 times thinner than a human hair. Courtesy of RUB, Marquard.

The researchers’ approach, which introduces covalent guanine quantum defect chemistry as a potential design concept for biosensors, has broad application and allows molecular sensors to be created without impairing fluorescence in the NIR. Although NIR light is not visible to the human eye, it is desirable for optical applications because the level of other signals in this range is highly reduced.

In earlier studies, the RUB team had shown how the fluorescence of nanotubes can be manipulated to detect vital biomolecules. The next step, involving researchers from IMS and ETH Zurich as well as RUB, was to customize the carbon sensors so they could be used with different target molecules in a straightforward manner.

To build the modular sensors, the researchers linked DNA bases to the nanotubes to create a guanine quantum defect in the crystal structure of the nanotube. The guanine quantum defect caused the fluorescence of the nanotubes to change at the quantum level.

The defect also acted as a molecular handle, which enabled the researchers to introduce a detection unit into the sensor, that can be adapted to a target molecule for the purpose of identifying a specific viral or bacterial protein. The interaction between the detection unit and a bacterial or viral molecule affects the fluorescence of the nanotubes, causing their brightness to increase or decrease.

The new sensor design resembles a “molecular toolbox” that can be used to quickly assemble sensors for a variety of purposes.

“Through the attachment of the detection unit to the DNA anchors, the assembly of such a sensor resembles a system of building blocks — except that the individual parts are 100,000 times smaller than a human hair,” said Sebastian Kruss, professor of physical chemistry at RUB. The NIR fluorescent biosensors are built from tubular carbon nanosensors with a diameter of less than 1 nm.

To demonstrate the potential of the biosensor, the researchers designed sensors for the SARS CoV-2 spike protein and used aptamers to bind to the protein. “Aptamers are folded DNA or RNA strands. Due to their structure, they can selectively bind to proteins,” researcher Justus Metternich said. “In the next step, one could transfer the concept to antibodies or other detection units.”

The fluorescent sensors indicated the presence of the SARS-CoV-2 protein with a high degree of reliability. The selectivity of sensors with guanine quantum defects was higher than the selectivity of sensors without the defects.

Experimental setup for producing the guanine defects: LEDs and the photosensitizer rose bengal are used to produce a reactive form of oxygen that can selectively link certain DNA bases to the nanotube. Courtesy of RUB, Marquard.

The sensors with guanine quantum defects were also more stable in solution. “This is an advantage if you think about measurements beyond simple aqueous solutions,” Kruss said. “For diagnostic applications, we have to measure in complex environments, for example, with cells, in the blood, or in the organism itself.”

The team’s approach to developing the sensors could provide a generic blueprint for the development of NIR fluorescent biosensors with improved stability.

The research was published in Journal of the American Chemistry Society (www.pubs.acs.org/doi/10.1021/jacs.3c03336).