In the five-capillary sequencer, excitation of the ABI FAM and JOE dye primers is accomplished using the 488 nm line of an argon ion laser. TAMRA and ROX dye primers are excited with the 543 nm line of a green helium-neon laser.  Because Raman scattering from the blue laser would increase the background in the TAMRA and ROX channels, a chopper wheel alternately blocks the blue and the green laser. Both lasers are aligned so as to pass just below the tips of the capillaries in the sheath flow cuvette by using a planoconvex lens and dichroic beam splitter. The fluorescent spots in the laser beam below the capillary tips are imaged onto 5 GRIN lenses with a microscope objective. In order to discriminate between the different dye primers the fluorescent emission is collected after passing it through four different bandpass filters. The fluorescence emission is transmitted from the GRIN lenses to avalanche photodiodes where it is measured and the intensity read by a computer. In this instrument the laser chopper must be timed precisely with the spinning filter wheel. Both filter and chopper wheels are driven by stepper motors that are controlled with homemade electronics and computer software.

       The figure below shows the image of the five fluorescent spots generated within the cuvette, panel A. The tips of the cuvette are barely visible as the reddish objects above the spots. A filter was used in the camera to block scattered laser light, and the excitation beam is invisible. We used a convenient trick to align the system. The fiber optics were disconnected from the photodiodes and illuminated with a lamp. Light traveled in the reverse direction through the system, and was observed with a microscope. The system was aligned so that the light from the illuminated fibers was co-incident with the fluorescent spots from the samples, panel B.

       This instrument was described in the paper "A multiple-capillary electrophoresis system for small-scale DNA sequencing and analysis" J.Z. Zhang, K.O. Voss, D.F. Shaw, K.P. Roos, D.F. Lewis, J. Yan, R. Jiang, H. Ren, J.Y. Hou, Y. Fang, X. Puyang, H. Ahmadzadeh, and N.J. Dovichi, Nucleic Acids Research 27, E36 (1999), where E36 refers to the electronic publication number for the paper.