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Arrays Advance DNA Detection

Photonics Spectra
Jul 2000
Michael D. Wheeler

Researchers from Tufts University have devised a screening method using a bead-based fiber optic array that could dramatically increase the speed and sensitivity of DNA sampling.

Despite the tremendous commercial success of DNA microarrays -- also known as DNA chips -- this method requires target labeling, a time-consuming, labor-intensive process. It can also affect the level of targets present in a sample, making measurements inexact.

David R. Walt, along with postdoctoral researcher Frank Steemers and graduate student Jane Ferguson, engineered a new type of microarray that uses oligonucleotide probes (tethered nucleic aids with known sequences) attached to tiny latex beads on optical imaging fibers. These tiny beads, also known as molecular beacons, bind to specific DNA sequences in a sample.

A new type of DNA microarray incorporates latex beads into a matrix of wells etched into an optical imaging fiber substrate. Such arrays could dramatically increase the speed and sensitivity of DNA sampling. Courtesy of Tufts University.

"The beacons contain both a fluorophore and a quencher that are close to one another when no DNA is bound," Walt said. "When DNA binds, the quencher is displaced and the fluorophore regains its fluorescence."

Once binding occurs, the researchers focus excitation light onto one end of the optical fiber, stimulating the fluorescent label on the distal end. Isotropically emitted light from the fluorophore captured by the fiber travels back to the other end where a detection system separates the excitation light signal from the emitted signal.

A Princeton Instruments PentaMax CCD camera and an Olympus microscope stage mounted horizontally are the chief components of the instrumentation used to record the signal. A Signal Analytics IPLab system on a Macintosh platform performs image processing and acquisition.

The use of latex beads in etched wells on the end of an imaging fiber has a number of advantages over existing DNA screening methods. The feature sizes of conventional microarrays are linked to the fabrication method. Feature sizes of the Tufts arrays, however, are determined by the intrinsic size of the latex beads.

Also, the Tufts approach allows relatively high-throughput capabilities and fast hybridization times with multiple probes. The number of different probes for specific DNA sequences or mutations can be extended easily by entrapping multiple fluorescing dyes or using a combination of dyes in the interior of the microspheres. And the small size of these beads enables preparation of billions of microspheres at a time.

Illumina Inc. in San Diego is working to commercialize the arrays.

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