DNA Biosentinels

DNA researchers are learning how to snag strands of DNA and examine them one by one under a microscope.

In a pot of boiling water, spaghetti's a tangled mess. But let's say you want to look at a piece more closely. Simple. Just hook a strand around the handle of a wooden spoon and it straightens out quite nicely. You can examine it easily.

NASA-supported bioengineer Susan Muller of UC Berkeley wants to do the same thing to DNA.

When researchers get a sample of DNA for analysis it's often a tangled mess of coiled strands - just like that pot of spaghetti. They analyse it by chopping the strands into pieces, cloning the fragments, sequencing the pieces, sorting them according to size and, finally, fitting them back together again. In short, it's a complex and time-consuming process.

Muller and colleague Eric Shaqfeh are working on a more straightforward procedure - a way to stretch out a single strand of DNA for examination by a standard laboratory microscope.

Why does NASA care? Because astronauts have DNA.

"Astronauts in space are exposed to radiation, and this can damage their DNA," explains Frank Cucinotta of NASA's Space Radiation Health Program. Of particular concern are heavy cosmic rays - the energetic nuclei of iron atoms, for instance - which can crash through DNA like little atomic cannonballs, causing complex breaks called "clustered DNA damage."

Credit OBPR An artist's concept of DNA battered by heavy ions from space.

"We know that cells on Earth have not evolved to be competent in repairing such damage," he says. New DNA analysis tools are needed "to study the problem and develop remedies."

To snag DNA for study, Muller uses a carefully devised fluid flow in a device just a few millimetres long. A flow device, with its tiny linked pools and channels, can be simple or maze-like in design. One that's shaped like a cross, for instance, with fluid flowing in through two arms and out through the opposite two, is very effective at stretching DNA. Muller's device is a bit more complicated than this; it not only stretches the DNA but also allows her to tag the DNA with fluorescent markers and to photograph the glowing strands.

The DNA she's working with is from a virus that infects bacteria. "It's a very popular DNA with bioengineers," she says. "It has about 48 thousand base pairs (or 48,000 rungs in the DNA ladder). Under quiescent conditions, if it's just floating in solution, it has a size of about .7 microns. But it you were to stretch it out completely, it would be about 22 microns in length" - about 10 times longer than a typical bacterium.