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Wednesday, September 24, 2008

The Portable DNA Detector

On-site CSI: After a blood sample is collected from the scene of a crime, this briefcase-sized device can be used to extract and analyze its DNA in six hours or less.
Credit: University of California, Berkeley

A new portable DNA analyzer performs real-time analysis of blood samples left at the scene of a crime. Researchers at the University of California, Berkeley, developed the device, which packs microfluidics, electronics, optics, and chemical detection technology into a single briefcase-sized unit. "While previous groups have developed lab-on-a-chip systems, none of them have succeeded in making a completely portable, robust system that can be used at a scene," says team leader Richard Mathies.

The new device can be used for short tandem repeat (STR) analysis, a technique that has become routine in modern forensic work since it was first applied in 1991, but one that normally takes place in the lab. The researchers carried out real-time STR profiling at a mock crime scene set up by the Palm Beach County Sheriff's Office. Blood stain samples were collected and DNA extraction and analysis were performed at the crime scene within six hours.

The researchers stress, however, that while their system is very reliable, it is not yet commercially available and can be used only to provide preliminary evidence for police investigations. "The advantage is that the police could now have almost immediate information on who the most likely criminal actually is," explains Mathies. "This enables them to find the person and get crucial evidence before he or she leaves the region or destroys evidence."

Mathies is the inventor of capillary electrophoresis arrays and energy-transfer fluorescent dye labels--two technologies commonly used in modern DNA sequencers. These technologies combine miniaturized chemical and biochemical analysis with high-sensitivity fluorescence detection.

After a sample is obtained at the scene of a crime, DNA strands are amplified and separated to detect a "signature." Inside the device, a DNA fragment is replicated within a 160-nanolitre polymerase chain reaction (PCR) reactor coupled with an on-chip heater and temperature sensor. The biological sample and PCR reagents are exposed to three distinct temperatures for a certain amount of time, and a seven-centimeter-long separation channel is used for analyzing DNA by capillary electrophoresis. Using the device, the researchers succeeded in producing reproducible STR profiles of DNA samples in as little as two-and-a-half hours.

The detector measures 30 by 25 by 10 centimeters and weighs 10 kilograms. It consumes 20 watts of power, which can be supplied by a car battery. "It can thus be easily carried in a suitcase and checked in as flight luggage," says team member Peng Liu.

One of the biggest challenges in designing a portable DNA sequencing device is controlling the flow of samples through the system. To overcome this issue, Mathies and coworkers built a multilayer plastic chip containing an intricate system of etched channels. This system was fabricated with using the same techniques used to manufacture computer chips.

Most U.S. states now collect DNA samples from suspects upon arrest. So the ability to quickly match crime scene samples with records from this database could dramatically speed up the identification of criminals, Mathies says.

The Berkeley team plans to improve the sensitivity and throughput of the device by integrating other analytical steps, such as post-PCR "cleanup." By integrating more units, it will be possible to analyze several DNA samples at the same time, explains Liu. The device could appear on the market in as little as three to five years, the researchers say.

"One of the barriers to developing lab-on-a-chip technology is systems and process integration, and it is this aspect of the new work that is really exciting," says Stephen Haswell of the University of Hull, UK, who is also working on crime-scene DNA matching. "The work is an important development for both the forensic community and those striving to develop truly lab-on-a-chip technology."