Move over, PCR. A new DNA detection technique may prove faster, cheaper and more portable.

Finding the DNA Needle in the Haystack

A magnet might be just the thing to pull the proverbial needle from the haystack, at least when it comes to plucking a specific DNA molecule from a vat of the stuff. A new technique based on magnetic beads is just as accurate as polymerase chain reaction (PCR) assays--the current gold standard for DNA detection--and could offer some new advantages for diagnostic tests and genetic research.

Ever since the advent of PCR in the mid-1980s, the technique has been the tool of choice for finding rare DNA molecules. Like a Xerox machine, the method reproduces the molecule of interest until there are enough copies to be detectable using other laboratory methods. But some of the copies are made from copies, yielding illegible results that limit PCR's accuracy.

The new method was developed by chemist Chad Mirkin and colleagues at Northwestern University in Evanston, Illinois, who modified a technique they'd used previously to detect tiny amounts of protein (ScienceNOW, 26 September 2003). Mirkin's team attached to microscopic gold beads various "bar code" DNA molecules, as well as a few strands that bind specifically to half of the DNA sequence of interest. They added these beads to the sample to be tested, and then added that mixture to a test tube containing magnetic beads coated with DNA strands that bind the other half of the DNA.

If the sequence of interest is in the sample, it forms a link between the gold beads and the magnetic beads. Applying a magnet pulls out the magnetic beads, along with any linked gold beads and their associated bar-code DNA. Because these extra DNA molecules only tag along with the sequence of interest in the sample, their presence--which can easily be detected with a standard test for DNA--indicates a positive result.

In a test run, the technique could detect one DNA molecule in 100 billion billion molecules, they report online 27 April in the Journal of the American Chemical Society. The method is at least as sensitive as PCR, Mirkin says, and more accurate--the team could also detect a change of a single letter in the DNA, a technically difficult feat for error-prone PCR. And unlike PCR, the technique does not require expensive machines and enzymes. Also, technicians can be trained in the method in less than an hour, making it perfect for fieldwork.

Mirkin says that within a few months his team will have diagnostic tests for several diseases that can be used in a doctor's office, without special equipment. But the real value of the work lies in its potential for genomic research, says chemist Shuming Nie of Emory University in Atlanta, Georgia. The assay can be used to create a "molecular profile" that reveals the presence of a gene and how much RNA and protein it has expressed all from the same sample--something that now requires three more complicated techniques.

Related site
Mirkin Research Group at Northwestern