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By capillary electrophoresis (CE) in miniaturized lab-on-a-chip devices, integrated DNA sequencing and genetic diagnostics have become feasible. We introduce a principle of parallel optical processing to significantly enhance analysis capabilities. In a commercial microfluidic chip, a plug of DNA molecules was injected and the DNA molecules were CE-separated with a high relative sizing accuracy of >99%. Through an optical waveguide inscribed by femtosecond-laser writing a laser was launched perpendicularly into the microfluidic channel. A photomultiplier collected the fluorescence signals from a small detection window with a limit of detection of ~8 DNA molecules. In our approach, different sets of exclusively end-labeled DNA fragments are unambiguously identified by simultaneously launching several continuous-wave lasers, each modulated with a different frequency, detection of the frequency-encoded signals at different fluorescence wavelengths by a single ultrasensitive, albeit color-blind photomultiplier, and Fourier-domain frequency decoding. As a proof of principle, fragments from independent human genomic segments, associated with genetic predispositions to breast cancer and anemia, are simultaneously analyzed in a single flow experiment. This novel method of modulation-frequency-encoded fluorescence excitation opens new opportunities in genetic diagnostics. It enables the identification of end-labeled DNA samples of different genetic origin during their electrophoretic separation, opening perspectives for intrinsic size calibration, malign / healthy sample comparison, and exploitation of multiplex ligation-dependent probe amplification.

We use direct femtosecond laser writing to integrate optical waveguides into a commercial fused silica lab-on-chip (LOC). We fabricate high quality waveguides intersecting the microfluidic channels and use them to optically address with high spatial selectivity their content. Fluorescence from the photoexcited volume is efficiently collected at a 90 degrees angle by a high numerical aperture fiber, resulting in a compact and portable setup. Our approach is quite powerful because it allows the integration of photonic functionalities, by simple post-processing, into commercial LOCs, fabricated with standard techniques. By taking advantage of the unique three-dimensional capabilities of femtosecond laser writing, more complex functionalities, such as splitters or Mach-Zehnder interferometers, can be implemented.