DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions/deletions from DNA fragments in the diagnostically relevant range of 150−1000 base-pairs requires a sizing accuracy of <i>S</i> < 10<sup>-3</sup>. Here we demonstrate <i>S</i> = 4×10<sup>-4</sup>. A microfluidic chip was post-processed by femtosecond-laser writing of an optical waveguide. 12 blue-labeled and 23 red-labeled DNA fragments were separated in size by capillary electrophoresis, each set excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue/red signals distinguished by Fourier analysis. Different calibration strategies were tested: a) use either set of DNA molecules as reference to calibrate the set-up and identify the base-pair sizes of the other set in the same flow experiment, thereby eliminating variations in temperature, wall-coating and sieving-gel conditions, and actuation voltages; b) use the same molecular set as reference and sample with the same fluorescence label, flown in consecutive experiments; c) perform cross-experiments based on different molecular sets with different labels, flown in consecutive experiments. From the results we conclude: Applying quadratic instead of linear fit functions improves the calibration accuracy. Blue-labeled molecules are separated with higher accuracy. The influence of dye label is higher than fluctuations between two experiments. Choosing a single, suitable dye label combined with reference calibration and sample investigation in consecutive experiments results in <i>S</i> = 4×10<sup>-4</sup>, enabling detection of single base-pair insertion/deletion in a lab-on-a-chip.
We report on the use of femtosecond laser pulses to fabricate photonic devices (waveguides and interferometers) inside
commercial CE chips without affecting the manufacturing procedure of the microfluidic part of the device. The
fabrication of single waveguides intersecting the channels allows one to perform absorption or Laser Induced
Fluorescence (LIF) sensing of the molecules separated inside the microchannels. Microfluidic channels, with access
holes, are fabricated using femtosecond laser irradiation followed by chemical etching. Mach-Zehnder interferometers
are used for label-free sensing of the samples flowing in the microfluidic channels by means of refractive index changes