PCR-free DNA-based biosensing with polymeric optical hybridization transduction using micro- and submicron-magnetic bead captured on micro-electromagnetic traps Sébastien Dubus 1 , Boris Le Drogoff 2 , Jean-François Gravel 1 , Denis Boudreau 1 and Teodor Veres (presenting) 2 * 1 Département de chimie et Centre d’Optique Photonique Laser (COPL) Université Laval, Qc, G1K 7P4, Canada; 2 Industrial Material Institute, National Research Council Canada 75, de Mortagne, Boucherville, Qc, J4B 6Y4, Canada * E-mail : teodor.veres@cnrc-nrc.gc.ca, Phone: (450) 641-5232, Fax: (450) 641-5105 ABSTRACT In this paper, we present results from an approach based on the rapid and selective capture of target nucleic acids grafted on probe-functionalized magnetic micro- and nanobeads using integrated micro-electromagnetic traps in a microfluidic platform, followed by real-time optical detection. The influence of the magnetic bead diameter, from 2.8-μm to 500-nm diameter beads, has been systematically investigated in term of particle mobility under magnetic field and fluorescence signal (S/N ratio). It is clearly shown that reducing the size of magnetic particles offers higher sensitivity for the optical detection but decreases the magnetic trapping efficiency and the dynamic range for the microfluidic flow. By optimizing both parameters, this technique allows the detection of a few hundred copies of bio-threat-specific DNA material in less than one hour without any chemical or enzymatic pre- amplification. Keywords: DNA-based biosensor, magnetic particles, magnetic confinement, electro-magnetic traps, PCR-free sensibility, Lab-on-a-Chip. 1 INTRODUCTION The interest in the development of fast and reliable sequence-specific DNA biosensors has grown tremendously over the past few years. Because the amount of DNA material to be detected is often extremely small, the need for a detection scheme capable of transducing the hybridization event with sufficient sensitivity has led to the investigation of a number of sensitive approaches. A strategy that has increased in popularity in recent years is the use of surface-functionalized magnetic particles to selectively bind low-abundance target analytes (DNA, bacteria or viruses) in order to preconcentrate them prior to the detection step [1-2]. These particles are available across a wide size range and offer large contact surfaces for specific functionalization, thus allowing the optimization of and separation procedures with relative ease of use. While the most effective way to concentrate these particles is still the use of macroscopic permanent magnets, recent reports have shown the possibility to effectively manipulate and control the motion of magnetic microbeads on the micron scale [3-5]. This offer the possibility to concentrate, confine and detect targeted analytes in a microscopic volume using magnetically "tagged" probes and very sensitive optical methods. Our approach uses magnetic microbeads functionalized with ssDNA probes and a fluorescent polymeric transducer that allow for the highly sensitive detection of target DNA without the need for any additional fluorescent DNA labelling [6]. This method involves three steps: 1) grafting the beads with a specific probe, 2) duplex formation on the beads’ surface and 3) hybridization of target on beads and detection following magnetic confinement. We recently demonstrated that this technique can be used to detect target DNA directly on magnetic particles while the micro-beads are being magnetically confined in a small volume by a micro-electromagnetic trap (μEMT) [7-8]. In this work, two different geometries of micro-electro- magnetic traps (μEMT) have been designed for the capture of functionalized magnetic beads on a microfluidic platform. A confocal fluorescence detection system has been used to perform “on-bead detection” at the center of the μEMT. A systematic investigation in terms of magnetic capture efficiency under magnetic field and hydrodynamic forces, and fluorescence signal as a function of bead size (from 2.8 μm to 500 nm) were performed. 2 EXPERIMENTAL 2.1 Fabrication of micro-electromagnetic trap devices The first studied generation of μEMT consists of a planar micron-scale current-carrying gold conductor based on a circular design described by C.S. Lee et al. [5]. We recently improved this design by adding, in a second generation of μEMT, a nickel micropost in the middle of the loop in order to concentrate the magnetic field and thus the magnetic force in the center of the traps [9]. Our microfabrication process method can be divided as follow: NSTI-Nanotech 2006, www.nsti.org, ISBN 0-9767985-7-3 Vol. 2, 2006 225