CHAMPAIGN, Ill. An inexpensive, real-time sensor technology harnesses living DNA to detect dangerous metals such as lead, mercury and cadmium.
Developed by researchers at the University of Illinois, the DNA sensors immediately react to the presence of specific metals by emitting light into an inexpensive fiber-optic lens. Traditional methods require lengthy batch testing or expensive instrumentation. Genetic algorithms were used to discover the specific required DNA strands required to detect specific metals from within a population of trillions of random DNA sequences.
Engineers could benefit from this method by designing their own DNA strands that would test in real-time for specific metallic substances.
"We have created a new class of simple and environmentally safe sensors the world's first example of a catalytic DNA-based biosensor with highly sensitive fluorescence detection for metals," said professor Yi Lu. Lu was assisted by graduate student Jing Li, co-author of their recent paper in the Journal of the American Chemical Society. The process patent is pending.
Lu's technology harnesses the human body's ability to detect specific kinds of molecules and orchestrate responses in real-time. This molecular recognition capability involves a "lock and key" mechanism in which custom-tailored receptor "pockets" will only accept specific molecules, and respond immediately when they do encounter the correct molecules. While the human body grows these specific receptor sites according to the blueprints contained in DNA, Lu decided to go straight to the source. "Our sensor's technology is unique, because the active element consists of small pieces of real DNA, the basic building block of all our genes," said Lu.
Lead and other dangerous environmental contaminants, such as industrial mercury and cadmium, can be detected today only after lengthy batch testing of samples for specific elements. Thus there is a need for a quick and inexpensive method for on-site, real-time testing for hazardous substances.
That capability has become a high priority at the National Institutes of Health, which provided the funding for Lu's experiments. The NIH has specifically targeted health applications for the technology, including environmental monitoring, clinical toxicology, wastewater treatment and industrial process monitoring.
Lu's innovation is based on a 1994 pharmaceutical discovery that DNA was not just a genetic information repository, but that DNA could also act in a manner similar to living enzymes that catalyze a specific chemical reaction right at the site where it is needed. As a result of this discovery, many promising new pharmaceutical agents have been demonstrated in which metal ions are essential to activate the catalytic function. These enzymes, called catalytic DNA, constitute a new class of metalloenzymes derived from metallo-nucleic acids. Lu's innovation was seeing how to turn this pharmaceutical discovery into a sensor technology.
Lu engineered a way to attach a fluorophore to one end of the DNA strand and a fluorescence quencher on the other end. In steady state when exposed to 560-nm light for excitation of the flourophore, the quencher's proximity keeps the fluorophore from glowing. But when the desired metal is present lead in his demonstration experiment it cleaved the quenching end, resulting in an easily detectable 400 percent increase in fluorescence. "DNA is stable, cost-effective and easily adaptable to optical-fiber and chip technologies," said Lu.
To turn his discovery into a working sensor technology, something the researchers have not yet done, they would attach the fluorophore end to a chip substrate designed to have an optical fiber permanently attached. Then when the quenching end is cleaved, it leaves the 400 percent increased fluorophore glowing directly into the fiber optic, indicating the presence of the hazardous metal. These chips could also be "reset" by washing off the sample and chemically reattaching new fluorescence quenchers for the same or a different metal to be detected.
To turn his theoretical biosensor into a working technology, Lu had to turn to genetic algorithms. While the 1994 discovery of catalytic DNA demonstrated its principle, now six years later, the process by which the base-four DNA codes (using A, C, G and T "bits") respond to specific molecular shapes is still a mystery. Theoreticians continue to speculate on the specific mechanisms at work, but an analytic understanding that would allow designers to specify particular A, C, G and T sequences as "locks" for specific metal "key" molecules is not yet possible. Rather than wait for the theoreticians to hash it out, Lu responded in typical engineer fashion, by appealing to genetic algorithm searching techniques to merely test millions of randomly generated DNA strands and select those that respond to the desired metal. Here is where Li took over doing the in-the-trenches work of generating trillions of different DNA stands in a test tube, then performing genetic algorithms to select the ones that happen to work for detecting lead.
Li implemented the genetic algorithm by first generating a massive population of 1 quadrillion random DNA strands individual strands that can fold like proteins, rather than the familiar intertwined double-helix that serves as a blueprint for living things.
A natural selection process then filtered out those strands that could only fold around lead, pictured as a DNA "pocket" that can only fit a specific molecular shape. This smaller population was then subjected to random mutations which were multiplied using polymerase chain reactions to create another large population, and the process repeated.
In the end, Li was able to obtain DNA strands that could detect lead over a concentration range of three orders of magnitude. Since the fluorescence domain is decoupled from the metal-recognition domain, by virtue of the quenching effect, Lu has high hopes that Li will someday be able to run improved genetic algorithms that further advance not only the sensitivity of specific catalytic DNA strands, but also make sure that no untested metal ions are around that could accidentally trip the system.