DNA Separation and Fluorescence Monitoring by Integrated Waveguides in an Optofluidic Chip C. Dongre, 1* J. van Weerd, 2 G.A.J. Besselink, 3 R. Martínez Vázquez, 4 R. Osellame, 4 R. Ramponi, 4 G. Cerullo, 4 R. van Weeghel, 2 H.H. van den Vlekkert, 3 H.J.W.M. Hoekstra, 1 and M. Pollnau 1 1 Integrated Optical Microsystems (IOMS), MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, *corresponding author: C.Dongre@ewi.utwente.nl 2 Zebra Bioscience BV, Wethouder Beversstraat 185, 7543 BK Enschede, The Netherlands 3 LioniX BV, P.O. Box 456, 7500 AL Enschede, The Netherlands 4 Istituto di Fotonica e Nanotecnologie (IFN-CNR), Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy We report on the monolithic integration of optical waveguides and microfluidics in a fused-silica lab-on-a-chip. Labeled biomolecules such as double-stranded DNA are flown and separated in the microfluidic channel by capillary electrophoresis and their fluorescent labels are excited by a continuous-wave laser beam through femtosecond- laser-written integrated waveguides. In this context, desirable features such as high spatial resolution (~12 μm), and a low limit of detection (~ 6 nano-molar) have been experimentally demonstrated. The proof of concept is being extended to real-world diagnostic samples for on-chip diagnosis of genetic diseases, e.g. breast cancer. Introduction Lab-on-a-chip (LOC) systems aim at miniaturizing and integrating functionalities of a biological/chemical laboratory into a microchip [1]. The use of integrated optical sensing for monitoring in LOC devices has seen a continuously growing demand [2]. Laser-induced fluorescence (LIF) is one of the most sensitive and widely used among different optical sensing techniques, especially in biological applications, owing to the wide availability of different fluorescent labeling schemes, which can selectively impart fluorescent properties to certain species of biomolecules. One important application, the separation of double-stranded DNA (dsDNA) molecules, is implemented in a number of diagnostic bioassays, e.g., for the detection of chromosomal aberrations. The most preferred technique for such diagnostic separation of dsDNA fragments is capillary electrophoresis (CE) [3], governed by differences in the electrophoretic mobility of the concerned species according to the fragment size and electric charge. CE separation and analysis performed in an on-chip-integrated microfluidic (MF) channel typically rely on bulky, bench-top optical excitation and detection instrumentation. This is in contrast with many advantages of an LOC system by strongly limiting device portability and is hindering the development of field applications. Compared with these experimental setups, direct integration of optical waveguides (WG) into a commercial LOC device, as presented in this paper, offers several advantages by reducing system size, complexity, and cost. Several approaches have been implemented for such optofluidic integration, based on WG fabrication by silica on silicon, ion exchange in soda-lime glasses, photolithography in polymers, and liquid-core WGs, etc [4]. In this work we shall focus on the unique monolithic approach based on femtosecond (fs-) laser material processing [5].