DNA Boosts Artificial Nose

Thursday, October 21, 2010 @ 12:10 AM gHale

An “artificial nose” that uses fluorescent compounds and DNA could accelerate the use of sniffing sensors into the area of mass production and could lead to detection of anything from milk gone bad to explosives.
By sticking fluorescent compounds onto short strands of the molecules that form the backbone of DNA, researchers at Stanford University produced tiny sensor molecules that change color when they detect certain substances. The sensors use existing technology for synthesizing DNA, and then go under a fluorescence microscope.
The color changes enable the new sensors to convey far more information than most other existing optical sensors, which typically just detect one specific molecule, said Eric Kool, professor of chemistry and senior author of a paper on the subject.
“We were blown away by how strong the color changes were,” Kool said. “One of the surprising findings was that we could tell the difference between four different organic vapors with just one sensor, because it would turn different colors with different vapors.”
The key to Kool’s versatile sensor molecules lies in the structure of DNA, the famous double helix that encodes the genetic blueprint for life, often described as looking like a twisted ladder. Two long parallel chains of sugar and phosphate molecules constitute the rails of the ladder, with the rungs made of pairs of molecules called bases. The arrangement of the bases, of which there are only four types, encodes the genetic data.
Kool’s team of researchers developed a new set of fluorescent replacements for the DNA bases – seven different ones they could choose from – to attach to the DNA backbone of the new sensor in place of the usual four. They used only a single helix, so the bases project out from a single twisted pole, ready to detect organic vapors.
Florent Samain, a postdoctoral researcher in chemistry and lead author on the paper, used DNA synthesis techniques to generate a library of all 2,401 possible ways the seven substitute molecules could combine in a string of four units.
The team then screened all the possible combinations for sensitivity to four different test substances – as vapors – that differed significantly in their structural and electronic properties.
One substance was a common aquatic herbicide, another a solvent in research and industrial applications, another an inhibitor of mold and bacteria in food and the fourth an ingredient in products ranging from shoe polish to pesticides, as well as in the preparation of explosives.
The researchers found multiple sensors that showed marked fluorescent responses when exposed to the four test substances. “This is our first try with vapors and it ended up working really well,” Kool said.
“What makes these sensors work exceptionally well is that the bases in DNA are stacked on one another, physically touching each other,” he said. “DNA bases talk to one another, electronically.”
That close physical contact also allows the compounds that Kool’s group attaches to the DNA backbone to communicate with each other, which is crucial to their functionality.
What is also crucial, the researchers found out, is the order of the compounds along the DNA backbone. Like the sequence of natural DNA, which varies among different animals, the different sequences of the artificial DNA sensors gave different color changes.
“We saw a couple of examples where we had the same components, but in a different order and got a different response,” Kool said. “So clearly they are talking to one another and whoever is next to someone else, it makes a difference.”
Having a large number of sensors available in a single device could broaden the application of the sensors from pure organic molecules such as the ones used in the tests to the many mixtures of molecules often encountered outside the laboratory.
Researchers hope to eventually pair their sensors with some type of portable device that would contain an inexpensive fluorescence microscope, which Kool said a number of other laboratories are already working on.
“We want to sense everything,” Kool said. “That is our ultimate goal.”

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