Despite the growing importance of DNA analysis, present methods are time consuming, costly, and labor intensive. David Walt, a professor in the department of chemistry at Tufts University (Medford, MA) hopes to change that with his bead-based fiber-optic microarray for DNA analysis. "We are trying to push the limits of detection and achieve the highest level of sensitivity that we can," says Walt. He and his associates have developed an optical biosensor that monitors the hybridization of tagged DNA sequences.
Walt's method uses fused, coherent bundles of optical fibers, with each bundle containing up to 50,000 individual fibers. By etching away part of the fiber cores, the researchers form a microscopic well on the endface of each fiber. These wells hold the DNA probes, which are specially prepared, 3-µm latex beads coated with a specified DNA strand. When researchers add a liquid suspension of beads to the etched fiber face of the fused bundle, capillary action causes one bead to drop into each well and holds it in place to form a high-density array of probes.
At this point, the array is ready for exposure to the DNA sample under test. The fluorescently labeled sample strands bind to their complementary probe DNA. Without a match, the sample strands do not bind. The researchers illuminate the array with a lamp, triggering fluorescence in the tagged samples. At that point, the fluorescent signal propogates through the fiber to a detector, indicating which probe DNA matches the sample under test.
Walt's process has caused quite a stir in the medical field. Many existing microarray methods, such as those incorporating ink-jet techniques and photolithographic probe synthesis methods, can only be used once. "We've had experiments where we've performed a hundred different assays with the same array with only a 2% signal differential," says Jason Epstein, one of Walt's graduate students. "This system is robust." Another benefit is the design flexibility offered by the arrays, Epstein says. As new DNA sequences of interest are identified, new probe microspheres are produced and added to the array.
These scanning force images show the etched face of an optical fiber imaging bundle. The first (a) is empty, and the second (b) contains complementary-sized microspheres. Each well diameter is approximately 3.1 µm.
Bead arrays are also more sensitive than conventional microarrays. "Each bead has about a million reactive sites on it," says Epstein. "Because we are working with such small sensors, we can develop a high local concentration of DNA molecules, making it easier to locate the one that we are looking for."
DNA analyses are expensive and time consuming, in part because of the need to prepare the sample using polymerase chain reaction (PCR) to amplify and tag each DNA sequence with a fluorescent label (see oemagazine, January 2001, page 34). Without exception, every microarray process requires this preparation, says Walt, but this process takes hours. Walt and his associates are working on ways to eliminate this step. "We would like to get away from this process and be able to detect DNA that has been isolated without any amplification," says Walt.
Although Walt's bead array is still in the experimental stages, Illumina (San Diego, CA) has licensed the technology from Tufts with plans for commercialization. Illumina's product will be formatted to investigate DNA differences that may enable prescription drugs to be tailored for a person's genetic makeup.
The first major commercial DNA microarray came out in 1992 or so, says Epstein. That year there may have been one reference to that device. This past year, that same device has been referenced close to 1000 times. "In less than a decade, this field and technology have just skyrocketed," he says. "It may sound like science fiction, but in the not-so-distant future, we could have a personal DNA microarray at our doctor's office that would test us for everything, such as our susceptibility to cancer or pharmaceutical drug effectivenesslike determining one's optimal allergy medication." oe