Genes vary from person to person in a lot of little ways, much as two cars of the same model can come with different options. But in genes, differences as small as a point mutation--the alteration of a single base pair--can lead to disease. Now scientists have developed an improved probe for detecting point mutations. The advance, described in next month's issue of Nature Biotechnology, could lead to more accurate screening of organ donors and identification of genetic targets for new drugs.
The new probe, designed by Lloyd Smith and his colleagues at the University of Wisconsin, Madison, is a variation on a standard technique for detecting genetic variations. It is composed of a single strand of DNA that binds to a complementary sequence in target DNA. Such probes, about 20 nucleotides long, sometimes bind loosely to sequences slightly different from the target sequence. To determine how tightly the probe binds, researchers heat it up to shake the probe loose; however, often there's only a few degrees difference between the "melting" temperature of a probe bound to the exact target sequence and one where there is a minor discrepancy.
Smith's group substituted one of the probe's bases with 3-nitropyrrole, a molecule that is shaped like a nucleotide but that doesn't bind to one on an opposite strand. They found that this "mismatched" probe had a 15-degree difference between the melting points of an exact and a wrong match, suggesting that it will be much easier for this kind of probe to distinguish true from false hits. Now it's up to other researchers to see how useful the new probe will be, Smith says. "This is the kind of thing that we want to toss out there and see what the community does with it," he says.
Some scientists are anxious to put the probe through its paces. Molecular geneticist Lisa Baumbach of the University of Miami says the technique should be useful in screening for inherited forms of breast cancer, for which researchers must use many probes to distinguish among multiple mutations in a gene. In addition, says Smith, the mismatched probes should prove useful in assessing the compatibility of an organ donor and a recipient, by allowing researchers to quickly identify which version of the complicated HLA gene each person possesses.