title: Combined microfluidic-optical DNA analysis with single-base-pair sizing capability.
abstract: DNA sequencing by microchip capillary electrophoresis (CE) enables cheap, high-speed analysis of low reagent volumes. One of its potential applications is the identification of genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant size range of 150-1000 base-pairs requires a variance ofσ2< 10-3. In a microfluidic chip post-processed by femtosecond-laser writing of an optical waveguide we CE-separated 12 blue-labeled and 23 red-labeled DNA fragments in size. Each set was excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue and red signals distinguished by Fourier analysis. We tested different calibration strategies. Choice of the fluorescent label as well as the applied fit function strongly influence the obtained variance, whereas fluctuations between two consecutive experiments are less detrimental in a laboratory environment. We demonstrate a variance ofσ2≈4 × 10-4, lower than required for the detection of single base-pair insertion or deletion in an optofluidic chip.
authors.affiliation: Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands; Department of Materials and Nano Physics, School of Information and Communication Technology, KTH-Royal Institute of Technology, Electrum 229, Isafjordsgatan 22-24, 16440 Kista, Sweden.
authors.forename: Markus
authors.initials: M
authors.lastname: Pollnau
authors.affiliation: Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands; Theoretical Electrical Engineering, University of Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Hammer
authors.affiliation: Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: Chaitanya
authors.initials: C
authors.lastname: Dongre
authors.affiliation: Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: Hugo J W M
authors.initials: HJ
authors.lastname: Hoekstra
keywords: (130.3120) Integrated optics devices; (170.3890) Medical optics instrumentation