Optical Fibers Test DNA

Brent D. Johnson

Detecting very small quantities of chemical or biological material for security and defense applications is fraught with problems, including the generation of false-positives and -negatives as a result of a lack of sensitivity or accidental contamination. One way to resolve this is to introduce redundancy, because although a single positive test may be questionable, 20,000 are indisputable. Researchers at David Walt Laboratory at Tufts University now have demonstrated the practicality of using a fiber optic microarray to detect samples across 50,000 individual sensors.

A 1-mm² bundle of 50,000 optical fibers (A) packs a lot of sensing power into a small space, enabling researchers to detect small quantities of chemical or biological materials. A magnification of the hexagonal bundle (B) reveals the close-packed arrangement of the 3-µm-diameter fibers. Adapted with permission from I. Biran and D.R. Walt, Analytical Chemistry, 2002, 74, 3046. ©2002 American Chemical Society.

Graduate student Jason Epstein explained that an optical fiber can be melted and pulled into a capillary with nanometer dimensions. In the application, the researchers melt and pull thousands of fibers simultaneously to produce a thick bundle of individual light pathways. A 1-mm² bundle contains as many as 50,000 fibers that are 3 µm in diameter. "There aren't too many platforms that can rival this sensor-packing density," he said.

Using an HF buffer solution, they expose the end of each fiber and make an etched well approximately 3 µm deep that can accommodate sensors such as DNA strands, bacteria or yeast cells. These sensors are embedded with dyes -- yielding an optical bar code -- so that the position of each sensor is known. When a sensor contacts a particular bio-agent or its labeled DNA, the system measures a fluorescent signal, and because each sensor is coded with dye, the researchers know which has been activated. Incorporating three dyes at five concentrations gives them the potential for hundreds of combinations.

To read the sensor array, the researchers employ a custom-fit Olympus BX61 microscope. "Typically, you need lasers and confocal optics for such low detection limits, but we are using standard equipment," Epstein said. The microscope uses a white-light source with a 75-W Xe arc lamp, a dichroic housing and a Hamamatsu CCD camera, but the detection limits are extremely low. A few molecules in one of the 3-µm wells produce a very high local concentration.

Epstein said that the newest and most versatile version of this approach employs a cell-based sensor that can detect changes in numerous types of bioagent spores or DNA-damaging agents.