Array detection speeds DNA sequencing

A new multichannel detection system for capillary electrophoresis could reduce the time needed to sequence an individual`s DNA, or genome, to as little as 68 days, according to Edward Yeung, director of the Ames Laboratory`s Environmental Science Program at the University of Iowa (Ames, IA). That is considerably faster than with current systems, which engage single-channel sequencers to analyze DNA fragments.

Sep 1st, 1995

Array detection speeds DNA sequencing

A new multichannel detection system for capillary electrophoresis could reduce the time needed to sequence an individual`s DNA, or genome, to as little as 68 days, according to Edward Yeung, director of the Ames Laboratory`s Environmental Science Program at the University of Iowa (Ames, IA). That is considerably faster than with current systems, which engage single-channel sequencers to analyze DNA fragments.

The experimental system combines the ability to excite multiple capillaries simultaneously with a highly sensitive array detector that uses random pixel addressing to image the fluorescence from the DNA samples. These factors provide both improved speed and high-accuracy measurement.

Previously, the rate-limiting process in sequencing the human genome was considered to be the time needed to separate DNA fragments in traditional slab-gel electrophoresis. Last year researchers developed capillary-array electophoresis, which uses gel-filled bundled arrays and greatly reduces the time necessary to complete the task (see Laser Focus World, June 1994, p.16). In addition to a time reduction, the capillary-array method measures lower-level concentrations of DNA fragments than before.

In the system built by Yeung and associates, several capillaries are excited simultaneously, further reducing the elapsed time and permitting even smaller DNA fragments to be read. An argon-ion laser is focused with a 10-cm-focal-length lens at the center of an array of fused-silica capillaries that has been immersed in water (see Fig. 1); the liquid allows the light to reach all the fragments at once, rather than shining on one at a time in progression.1 Yeung`s experimental device used 100 capillaries, but he believes 1000 or more can be excited simultaneously using the same system.

Once the capillaries are excited, a charge-injection device camera detects each DNA fragment. To date, charge-injection device (CID) detectors have been used mainly in astronomy and atomic spectroscopy applications, but they offer a variety of advantages, including random pixel addressing, antiblooming capabilities, and high quantum yield over a wide wavelength range, that make them attractive as capillary electrophoresis detectors.2

For this application, a 512 ¥ 512-pixel-imaging CID is installed in a Dewar so the camera can be cooled using liquid nitrogen; a f/1.4 lens is attached to the CID camera head, and an extension tube between the lens mount and the lens allows for different magnification factors.

Random pixel addressing permits the camera to record information from the strongest fragments first, then the lower-level fragments are detected as the charge builds. Antiblooming imaging keeps the smaller fragments from being washed out by blooming--or spilling over--from other fragments. This characteristic allows more fragments to be read, providing a higher overall yield and more accuracy.

The technique for doing capillary electrophoresis with array detection was recently licensed by Premier American Technologies Corp. (PATCO, Bellefonte, PA). The company plans to have an instrument available sometime in 1996, with a price in line with research bud

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