Fluorescence Multiplexing with Time-Resolved and Spectral Discrimination Using a Near-IR Detector

We report on the design and performance of a two-color, time-resolved detector for the acquisition of both steady-state and time-resolved fluorescence data acquired in real time during the capillary gel electrophoresis separation of DNA sequencing fragments. The detector consisted of a pair of pulsed laser diodes operating at 680 and 780 nm. The diode heads were coupled directly to single-mode fibers, which were terminated into a single fiber mounted via a FC/PC connector to the detector body. The detector contained a dichroic filter, which directed the dual-laser beams to an objective. The objective focused the laser light into a capillary gel column and also collected the resulting fluorescence emission. The dual-color emission was transmitted through the dichroic and focused onto a multimode fiber (core diameter 50 microm), which carried the luminescence to a pair of single-photon avalanche diodes (SPADs). The emission was sorted spectrally using a second dichroic onto one of two SPADs and isolated using appropriate interference filters (710- or 810-nm channel). The dual-color detector demonstrated a time response of 450 and 510 ps (fwhm) for the 710- and 810-nm channels, respectively. The mass detection limits for two near-IR dye-labeled sequencing primers electrophoresed in a capillary gel column were found to be 7.1 x 10(-21) and 3.2 x 10(-20) mol (SNR = 3) for the 710- and 810-nm detector channels, respectively. In addition, no leakage of luminescence excited at 680 nm was observed in the 810-nm channel or 780-nm excited luminescence into the 710-nm channel. An M13mp18 template was sequenced in a single capillary gel column using a two-color, two-lifetime format. The read length was found to be 650 base pairs for the test template at a calling accuracy of 95.1% using a linear poly(dimethylacrylamide) (POP6) gel column, with the read length determined primarily by the electrophoretic resolution produced by the sieving gel.