Suz-Kai Hsiung 1 Che-Hsin Lin 2 Gwo-Bin Lee 1 1 Department of Engineering Science, National Cheng Kung University, Taiwan 2 Department of Mechanical and Electro-mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan A microfabricated capillary electrophoresis chip with multiple buried optical fibers and microfocusing lens for multiwavelength detection We present a new microfluidic device utilizing multiwavelength detection for high- throughput capillary electrophoresis (CE). In general, different fluorescent dyes are only excited by light sources with appropriate wavelengths. When excited by an appropri- ate light source, a fluorescent dye emits specific fluorescence signals of a longer wavelength. This study designs and fabricates plastic micro-CE chips capable of per- forming multiple-wavelength fluorescence detection by means of multimode optic fiber pairs embedded downstream of the separation channel. For detection purposes, the fluorescence signals are enhanced by positioning microfocusing lens structures at the outlets of the excitation fibers and the inlets of the detection fibers, respectively. The proposed device is capable of detecting multiple samples labeled with different kinds of fluorescent dyes in the same channel in a single run. The experimental results demonstrate that various proteins, including bovine serum albumin and b-casein, can be successfully injected and detected by coupling two light sources of different wavelengths to the two excitation optic fibers. Furthermore, the proposed device also provides the ability to measure the speed of the samples traveling in the microchannel. The developed multiwavelength micro-CE chip could have significant potential for the analysis of DNA and protein samples. Keywords: Capillary electrophoresis / Microlens / Miniaturization / Multiwavelength detection DOI 10.1002/elps.200410034 1 Introduction Microcapillary electrophoresis (CE) chips fabricated using micromachining techniques have considerable potential for use in the analysis of biological molecules, such as proteins and DNA. Compared to their conventional coun- terparts, micro-CE chips have the advantages of a higher separation efficiency, physically smaller dimensions, reduced sample and reagent consumption, lower applied voltage requirements, and higher detection limits. Micro- CE chips generally employ a laser-induced fluorescence (LIF) detection mechanism since this method enhances both the selectivity and the sensitivity of the device [1-5]. Traditionally, chip-based CE is performed under a high magnification microscope equipped with a single fluo- rescent light source and an optical detector. It has been reported that this scheme enables an excellent detection limit to be achieved (,10 211 M). However, the LIF system is bulky and the experimental procedure tends to be inef- ficient since only one type of labeled samples can be detected within a single test run. Furthermore, achieving a precise alignment of the various optical components is time-consuming and complicated. Hence, a requirement exists to utilize micromachining technologies to fabricate a miniaturized optical detection system capable of executing the high-throughput analysis of biomolecules, such as protein and DNA. Embedding optical waveguides/fibers within microfluidic devices offers a promising approach for reducing the size of the optical detection system. Several methods have been reported in the literature for the microelectro- mechanical system (MEMS)-fabrication of micro-optical waveguides. For example, the use of sol-gel processes to fabricate low-loss planar optical waveguides was report- ed by Yang et al. [6]. An integrated optical circuit using multiple planar waveguides has also been demonstrated utilizing organo-mineral materials [7]. Buried optical waveguides circuits could be realized on glass substrates using a simple UV exposure process. Meanwhile, a straightforward hot-embossing technique has been pre- sented for the fabrication of integrated planar waveguide Correspondence: Dr. Gwo-Bin Lee, Department of Engineering Science, National Cheng Kung University, Taiwan 701 E-mail: gwobin@mail.ncku.edu.tw Fax: 1886-6-2761687 Abbreviations: BOE, buffered oxide etchant; MEMS, microelec- tromechanical system; PMMA, poly(methylmethacrylate); SEM, scanning electron microscope 1122 Electrophoresis 2005, 5, 1122–1129  2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim