title: Quantification of rolling circle amplified DNA using magnetic nanobeads and a Blu-ray optical pick-up unit.
abstract: We present the first implementation of a Blu-ray optical pickup unit (OPU) for the high-performance low-cost readout of a homogeneous assay in a multichamber microfluidic disc with a chamber thickness of 600 μm. The assay relies on optical measurements of the dynamics of magnetic nanobeads in an oscillating magnetic field applied along the light propagation direction. The laser light provided by the OPU is transmitted through the sample chamber and reflected back onto the photo detector array of the OPU via a mirror. Spectra of the 2nd harmonic photo detector signal vs. the frequency of the applied magnetic field show a characteristic peak due to freely rotating magnetic nanobeads. Beads bound to ~1 μm coils of DNA formed off-chip by padlock probe recognition and rolling circle amplification show a different dynamics and the intensity of the characteristic peak decreases. We have determined the optimum magnetic bead concentration to 0.1mg/mL and have measured the response vs. concentration of DNA coils formed from Escherichia Coli. We have found a limit of detection of 10 pM and a dynamic range of about two orders of magnitude, which is comparable to the performance obtained using costly and bulky laboratory equipment. The presented device leverages on the advanced but low-cost technology of Blu-ray OPUs to provide a low-cost and high-performance magnetic bead-based readout of homogeneous bioassays. The device is highly flexible and we have demonstrated its use on microfluidic chambers in a disc with a thickness compatible with current optical media mass-production facilities.
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Marco
authors.initials: M
authors.lastname: Donolato
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Paula
authors.initials: P
authors.lastname: Antunes
authors.affiliation: Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden.
authors.forename: Teresa Zardán Gómez
authors.initials: TZ
authors.lastname: de la Torre
authors.affiliation: Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: En-Te
authors.initials: ET
authors.lastname: Hwu
authors.affiliation: Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan.
authors.forename: Ching-Hsiu
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Robert
authors.initials: R
authors.lastname: Burger
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Rizzi
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Filippo Giacomo
authors.initials: FG
authors.lastname: Bosco
authors.affiliation: Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden.
authors.forename: Maria
authors.initials: M
authors.lastname: Strømme
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark.
authors.forename: Anja
authors.initials: A
authors.lastname: Boisen
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kgs. Lyngby, Denmark. Electronic address: Mikkel.hansen@nanotech.dtu.dk.
authors.forename: Mikkel Fougt
authors.initials: MF
authors.lastname: Hansen
mesh_terms: D015374:Biosensing Techniques; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D004261:DNA Replication / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D056656:Lab-On-A-Chip Devices; D060328:Magnetic Phenomena; D046210:Microfluidic Analytical Techniques
chemical_list: D004247:DNA
keywords: DNA amplifications; Lab-on-a-chip; Magnetic biosensing; Molecular diagnostics; Optical scattering