A simple, cheap DNA detector – made in Canada

Richard Strafehl spent a year and a half scouring the world for a cheap‚ quick‚ reusable DNA detector. He found it right back where he started in Toronto.

Mr. Strafehl‚ chief executive officer of a start–up company called Safeguard Biosystems‚ traveled to the University of Texas two years go to check out a new sensor developed there. He was hoping to license the technology to create a fast and inexpensive method to look for specific DNA.

Not satisfied with what he found there‚ he continued his search‚ going as far abroad as Germany and Finland. And the technology was at home the entire time.

“Through a process of elimination‚ I ended up on Dr. [Ulli] Krull’s doorstep‚ and I’m very pleased that I happened to find this type of technology right in my own backyard‚” Mr. Strafehl says.

A University of Toronto chemist‚ Dr. Krull has created an extremely sensitive DNA detector. The technology isn’t fully developed yet‚ but already his device shows promise for use in food safety‚ the identification of genetic disorders‚ and possibly even the detection of the AIDS virus earlier than is now possible.

Essentially‚ his device consists of a fibre–optic strand that‚ when dipped into a solution‚ lights up if a specific piece of DNA is detected.

Dr. Krull has been working toward this goal since about 1998. “[Now] we have a system that could be made into a commercial product‚” he says.

Already‚ Alex Mackenzie‚ a pediatrician and geneticist at the Children’s Hospital of Eastern Ontario‚ is developing ways to use Dr. Krull’s sensor.

Dr. Mackenzie studies spinal muscular atrophy‚ an inherited genetic disease. As with Lou Gehrig’s disease‚ the nerves that control muscles spontaneously die‚ resulting in paralysis and death – usually by the age of 2.

There is at present no way to replace the lost nerves‚ but preventive treatment should be available within two or three years. However‚ doctors still lack a reliable way to screen newborns for spinal muscular atrophy.

“By the time the parents notice that the baby is no longer turning‚ most of the motor neurons have already died‚” Dr. Mackenzie says. “So about five years ago‚ I decided that I wanted to find a robust DNA–based way of screening newborns for spinal muscular atrophy‚ and a number of independent strands let me to [Dr. Krull]. He’s got a very special hammer‚ I’ve got my own special nail.”

Dr. Mackenzie hopes to be able to have a working prototype to screen newborns for the DNA responsible for this disease within a year and a half.

DNA is the material that all life uses to record instructions for how to build a living organism. It essentially consists of long strings of chemical code that spell out genes‚ recipes for making biological matter. A string of DNA is almost always attached to another complementary strand‚ which matches the code.

DNA‚ whether in a blood sample or in the bacteria in a vial of river water‚ is usually extremely difficult to analyze because there are so many other kinds of matter present. So most of the methods currently used to look at the genes require special machinery that makes thousands of copies of the DNA to bring the concentration up to a detectable level.

But this is time–consuming‚ and can be expensive – a single machine can cost up to $150‚000. Plus the chips the DNA is placed on “are tossed out after one use at tremendous expense‚” Dr. Mackenzie says.

Dr. Krull‚ like many scientists‚ has devoted much of his professional life to the development of a cheap‚ reusable DNA detector. But despite the years of research necessary to create this sensor‚ it is fairly simple.

The basis for the device is an optical fibre‚ a very thin bundle of glass threads that use light to transmit information. Optical fibres are already widely used for phone lines and Internet connections.

Using sticky molecules‚ a single piece of DNA‚ which has been separated from its complementary strand‚ is attached to one end of the fibre. An orange dye is attached to the other end of the DNA strand. This probe DNA could be anything‚ such as the gene for cystic fibrosis.

A biological sample‚ such as a culture of bacteria or a throat swab‚ is shocked with ultrasound. This breaks apart the cells‚ and chops up the long strands of DNA into smaller pieces‚ allowing the genetic material to scatter through the sample.

Then‚ all you have to do is stick the tip of the fibre–optic strand into the solution. If the DNA that matches the probe is present‚ it will be attracted to its partner‚ like a magnet.

When the two strands join‚ they set off a chemical reaction in the orange dye at the end of the probe DNA‚ causing it to glow. The orange light travels up the optical fibre‚ which‚ like a fake Christmas tree‚ glows orange at the other tip.

“Within seconds‚ we can process an E. coli culture – we just burst the cells and stick in our probes and see if we get a signal‚” Dr. Krull says.

He is not the only scientist looking at fibre–optic biosensors; many have examined this area since the devices were used in the 1970s to monitor carbon dioxide levels in pharmaceutical processing. However‚ few researchers have been able to come up with practical and reliable sensors.

“In general‚ the fibre–optic sensor hasn’t had the promise that some of the early projections would have thought‚” says Fred Milanovich‚ a biosensor researcher with Lawrence Livermore National Laboratories‚ a national security lab in the United States. But “Dr. Krull’s method for measuring [DNA] is a pretty powerful thing…I could see this as being quite cost–effective.”

Once in use‚ these fibres should be so sensitive to trace amounts of DNA that using them will not require the DNA to be amplified‚ doing away with the expensive equipment. Moreover‚ these fibres are reusable – some can be used more than 500 times.

“If Ulli can make a technology that does not use amplification‚ that is reusable and does a pretty impressive test‚ then the world will beat a path to his door‚” Dr. Mackenzie says.

The bacterial content of animals entering a slaughterhouse or the air supply of a subway system could be monitored for months with a single fibre. And because the fibres are so sensitive‚ they could detect DNA at levels that are difficult to measure‚ such as HIV in a newly infected person.