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Ultrafast DNA Nanosensor

A new type of sensor makes diagnosing infections quick and easy.
October 5, 2009

A portable instrument based on an ultrasensitive nanoscale sensor could detect bacteria in minutes, helping to catch infectious diseases early and prevent their spread. The simple, low-cost device should be available within three years, says Benjamin Miller, professor of dermatology and biomedical engineering at the University of Rochester Medical Center, and codeveloper of the sensor.

Glowing DNA: A CCD camera sensor captures the glow of hairpin-shaped DNA nanosensors when they bind with a target gene sequence of anthrax bacteria.

Right now, diagnosing common bacterial infections requires growing cultures in a laboratory over a period of days, but diagnosis could be greatly speeded by a number of new sensors based on various nanomaterials that are being developed for ultrasensitive, rapid DNA detection. The new instrument would take from 15 minutes to two hours for a diagnosis and could be used in doctor’s offices, hospitals, and homes.

Each sensor is a hairpin-shaped strand of DNA, complementary to the genetic sequence being targeted, that is fixed on a gold film. Gold quenches the glow of a fluorescent molecule attached to one end of the DNA. The DNA stays folded over until a target genetic sequence links to it. Its unfolding results in the fluorescent molecule moving away from the gold film and glowing, which can be seen under a fluorescent microscope.

Lighthouse Biosciences in West Henrietta, NY, is commercializing disposable cartridges to be used with the nanosensor technology. A blood or urine sample to be tested would be placed directly on the cartridge. The cartridge will be a lab-on-a-chip, with rapid, miniaturized ways to prepare the sample for testing. “In the cartridge there are steps for cleaning up samples, that is, extracting material you’re interested in and amplifying the [bacterial] DNA,” Miller says. The cartridge will then be placed in a small portable instrument that does the fluorescence imaging and analysis. Each cartridge should cost a few dollars, Miller says.

By attaching different DNA strands on the gold film, the same cartridge could screen for multiple pathogens, Miller says. So far, the researchers have made a sensor to detect antibiotic-resistant staph bacteria that cause skin infections. They are now working on detecting bacteria responsible for common urinary-tract infections. The sensors could also be used to quickly spot bacteria in food or bioterror agents in water supplies, or even to screen for genetic disorders or cancer.

In a newer version of the sensor, Miller and colleagues stick DNA strands on silver nanoparticles. The silver nanoparticles make the fluorescent signal 10 times brighter. Plus, because thin layers of silver nanoparticles are transparent, the sensor could be coated on glass and optical fibers to make new types of detecting instruments, Miller says.

DNA detector: A new ultrafast DNA sensor contains hairpin-shaped DNA strands attached to a gold film. The DNA unfolds when it captures the target gene sequence, and an attached fluorescent molecule glows.

In the other nanosensors being developed for ultrasensitive, rapid DNA detection, researchers are using carbon nanotubes, nanowires, and nanoparticles. All of these approaches promise high accuracy, portability, and low cost. “If you could make a portable device that would sit in your doctor’s office, then, using a small amount of fluid, your doctor could screen you for a genetic abnormality,” says Michael Strano, a chemical engineering professor at MIT who has made nanotube sensors that detect DNA electrically.

Nanosphere in Northbrook, IL, which makes a DNA nanosensor based on research by Northwestern University chemistry professor Chad Mirkin, is far ahead of the game. The Food and Drug Administration has already approved the company’s sensors for certain genetic and infectious diseases, and additional versions are pending FDA approval or in clinical trials.

Nanosphere’s sensor is a microarray coated with DNA strands complementary to the target DNA and incorporated into a test cartridge. Gold nanoparticles, also coated with complementary DNA, are introduced, followed by target DNA, which binds to both the microarray and a nanoparticle. Then the nanoparticle is coated with silver to amplify the light that is scattered from the particle; the light is captured using a digital camera sensor. This method of detection is 100,000 times more sensitive than detecting fluorescence, says William Moffitt, CEO of Nanosphere.

Miller calls Nanosphere’s technology fantastic. However, he adds, Lighthouse Biosciences’s diagnostics test is simpler and requires fewer steps.

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