New 'DNA chip' rapidly detects, identifies dangerous pathogens

April 14, 2003

Detecting pathogens, whether from natural diseases or biological weapons, is about to get faster and more convenient, thanks to a new technique that can sense harmful DNA and immediately alert a doctor or scientist. The research, published in the April 9 issue of the Journal of the American Chemical Society, uses custom-designed loops of DNA that emit colored light in the presence of a specific creature's DNA. The loop-laden chip could be used to detect anything from a bacterium or virus, to the specific DNA of a plant or person.

"More than ever we need ways to analyze genetic material quickly, whether it's to detect an infection in a patient or identify a potentially dangerous biological substance," says Todd Krauss, assistant professor of chemistry and co-creator of the chip. "We've designed a simple method that decreases the time, cost and quite possibly the potential for error inherent in the complicated techniques used today."

The new chip is remarkable in that it eliminates many of the time-consuming steps normally taken in identifying an organism by its DNA. Traditionally, workers in a laboratory have to make thousands of copies of a piece of DNA they want to test. Then a complex series of steps must be performed to attach a special molecule to the DNA, which will act as a fluorescent beacon, making the DNA strand easy to detect. These beacon-outfitted pieces are then mixed with control DNA sequences to see if any match. Matching sequences would adhere to one another, betraying their presence via the beacon.

The Rochester team, Krauss and Benjamin Miller, associate professor of dermatology, and student Hui Du, has created a new technique that is far simpler. A scientist might only have to place a drop of the solution in question onto a small chip or card and watch for a change of color to indicate whether specific DNA is present. The chips are sensitive enough that copying may be unnecessary, as are complex beacon attachments, and the chips could be easily manufactured so doctors could instantly detect dozens or hundreds of pathogens right in their office. Future soldiers would also be able to identify unknown biological substances quickly and surely on the battlefield.

A chip using the new method would be constructed like a field of wilted sunflowers--customized sequences of DNA are bent like hairpins, with one end "planted" into a layer of metal and the other end hanging down alongside it. This dangling end contains a molecule called a flourophore, which, like the brilliant head of a sunflower, shines brightly when properly lighted. With all of the sunflowers' heads bent down to the ground, the field as a whole looks green because the fluorophore is short-circuited when directly on the metal. When "watered" with the right DNA sequence, however, the flowers stand erect, turning the entire field--and thus the chip--from green to bright yellow.

The unfolding of the chip's detector DNA strands happens when new DNA with a precise sequence is dripped onto the chip. The chip's DNA is designed to prefer to be bonded with a specific DNA sequence, such as a sequence unique to anthrax, than to remain folded over on itself. The new DNA bonds along the length of many of the chip's DNA and the two form a sort of rigid stem that lifts the beacon. The all-important beacon is pre-attached to the detector strand of DNA, rather than needing to be attached to each and every strand of DNA being tested.

Currently, the Rochester team has developed chips that can detect an antibiotic-resistant type of stalph bacteria, and they're working on chips that can detect the non-antibiotic-resistant strain as well. A laser is also needed at present to highlight the "sunflower head," but Miller and Krauss are working on ways to make the signal from the beacon more easily visible.

"We're also developing a microarray version of this chip," says Miller. "Ultimately, we'd like to design chips that could detect several different kinds of pathogens at once."

This research was funded by Evident Technologies, Inc, by the University of Rochester's Center for Future Health, and by the New York State Office of Science, Technology, and Academic Research.
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University of Rochester

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