[tt] technologyreview: single-stranded DNA as generic molecule detector

[Alejandro Dubrovsky]

(
http://www.technologyreview.com/printer_friendly_article.aspx?id=20095
)

Wednesday, January 23, 2008
DNA-Based Artificial Nose
Single-stranded DNA can be used to identify explosives and other
airborne compounds.
By Brendan Borrell

Scientists have found a way to quickly identify which DNA sequences are
ideal for detecting a particular odor and turn dried DNA into odor
detectors. While many researchers are working on an electronic nose to
detect toxins and explosives, this new platform could be used to create
a wide array of sensors using existing high-throughput molecular-biology
equipment.

"Now what we can do is take a microarray of 20,000 sensors ... and pick
out those sensors that best respond to the odors of interest," says lead
researcher Joel White of Cogniscent, a company based in North Grafton,
MA, that manufactures odor-detection devices.

Compared with man-made sensor technologies developed for vision and
hearing, our ability to mimic the chemical senses--smell and taste--is
relatively primitive. To detect explosive materials such as TNT,
scientists typically design highly specific polymers that fluoresce when
they come in contact with their target compounds. But building a more
generalized electronic nose platform that could detect a wider range of
chemicals hasn't been possible.

Over the past decade, White and neuroscientist John Kauer of Tufts
University have been working to improve their patented electronic nose,
a handheld device that contains an array of 16 sensor types made of
synthetic polymers. These polymers are cross-reactive, so that several
sensor types may change shape in response to a single odor--a design
analogous to the human nose. The polymers are dyed with a fluorescent
marker, and their activation patterns can be monitored via optical
electronic sensors and analyzed by an embedded microprocessor. But after
10 years of hard work, the pair had only been able to incorporate about
50 synthetic polymers--far less than the estimated 1,000 sensors in a
human nose, which can respond to some 10,000 different odors.

Several years ago, the duo decided to test DNA--a natural polymer that
is ubiquitous in the biological laboratories where the scientists spend
most of their time. "When we first started talking about it with people,
nobody imagined that dye-labeled DNA dried onto a substrate would
respond to odors," says White.

The scientists began their experiments haphazardly: by scavenging short
pieces of single- and double-stranded DNA from neighboring labs at Tufts
and looking at their responses to several standard compounds. Their
first experiments with dye-labeled double-stranded DNA gave them a hint
that the approach could work, but all the sequences they tried responded
to odors in the same way.

Single-stranded DNA, on the other hand, provided repeatable responses to
odors, and this response depended on the specific sequence of four
amino-acid types that make up the genetic code. With a typical sequence
about 20 amino acids long, the team has the potential to create millions
of sensor types. In the current issue of PLoS Biology, the researchers
describe the response of just 30 sequences, but White says that now they
have identified hundreds of useful DNA sequences, including one that
responds to the vapor signature of TNT-containing land mines--an unusual
finding indicating the versatility of the technique.

Alan Gelperin at Philadelphia's Monell Chemical Senses Center hails the
discovery as a major step. "The whole field has been hindered by a lack
of diverse sensor technology," he says. "This is the first demonstration
that [DNA] could be used in this way." Since first learning of the
approach during a conference, Gelperin has collaborated with University
of Pennsylvania physicist Charlie Johnson to take the concept one step
further by incorporating an electronic readout made with carbon nanotube
transistors.

For now, White says that his team has incorporated his DNA sensors
alongside the synthetic polymers in targeted projects, including one
device for detecting ammonia gas, which would be useful for warning
emergency responders at toxic spills or for monitoring pollution from
livestock operations. He says that there is even interest among vintners
in developing a device that could help sniff out counterfeit wines.
"This was news to me," White says, laughing.
Copyright Technology Review 2008.