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Proceedings Paper

Highly sensitive measurement of single DNA translocation through an ultraviolet light spot on silicon nanopore
Author(s): Hirohito Yamazaki; Shinji Kimura; Mutsumi Tsukahara; Shintaro Ito; Keiko Esashika; Toshiharu Saiki
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Paper Abstract

Nanopore-based sensing is an attractive candidate for developing single-molecule DNA sequencing technology. Recently, optical detection with a parallel nanopore array has been demonstrated. Although this method is a promising approach to develop high thorough-put measurement, the approach requires observation at low-background condition. In this paper, we propose a new optical method for nanopore DNA sequencing with high resolution and a high signal-tonoise ratio. We use ultraviolet light for the excitation of a fluorescent probe and a nanopore in a silicon membrane. Because silicon has a large refractive index and an extinction coefficient at ultraviolet wavelengths, light transmission thorough the membrane is negligible. This contributes to low background measurement of fluorescence from fluorophore-labeled DNA strands. In addition, the z-polarization component of the electric field is attributed to generating a large electric field gradient at the nanopore exit due to its boundary condition at the silicon surface. Our numerical electromagnetic simulation revealed that the z-component electric field was dominant compared to the xcomponent electric filed. The intensity of the electric field increased steeply in 2 nm, when ultraviolet light of 375nm wavelength was focused on a 10nm-thick silicon membrane with a 7 nm-diameter nanopore. This steeply increasing electric field can be sufficient resolution for the sequencing of designed DNA polymer. Finally, our experimental results demonstrated optical detection of single DNA translocation events with a high signal-to-noise ratio under applied voltage.

Paper Details

Date Published: 20 February 2014
PDF: 8 pages
Proc. SPIE 8954, Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI, 895407 (20 February 2014); doi: 10.1117/12.2036648
Show Author Affiliations
Hirohito Yamazaki, Keio Univ. (Japan)
Shinji Kimura, Keio Univ. (Japan)
Mutsumi Tsukahara, Keio Univ. (Japan)
Shintaro Ito, Keio Univ. (Japan)
Keiko Esashika, Keio Univ. (Japan)
Toshiharu Saiki, Keio Univ. (Japan)

Published in SPIE Proceedings Vol. 8954:
Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI
Alexander N. Cartwright; Dan V. Nicolau, Editor(s)

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