Highly sensitive measurement of single DNA translocation through an ultraviolet light spot on silicon nanopore

Hirohito Yamazaki; Shinji Kimura; Mutsumi Tsukahara; Shintaro Ito; Keiko Esashika; Toshiharu Saiki

doi:10.1117/12.2036648

20 February 2014 Highly sensitive measurement of single DNA translocation through an ultraviolet light spot on silicon nanopore

Hirohito Yamazaki, Shinji Kimura, Mutsumi Tsukahara, Shintaro Ito, Keiko Esashika, Toshiharu Saiki

Author Affiliations +

Proceedings Volume 8954, Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI; 895407 (2014) https://doi.org/10.1117/12.2036648
Event: SPIE BiOS, 2014, San Francisco, California, United States

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.

Citation Download Citation

Hirohito Yamazaki, Shinji Kimura, Mutsumi Tsukahara, Shintaro Ito, Keiko Esashika, and Toshiharu Saiki "Highly sensitive measurement of single DNA translocation through an ultraviolet light spot on silicon nanopore", Proc. SPIE 8954, Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI, 895407 (20 February 2014); https://doi.org/10.1117/12.2036648

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KEYWORDS

Silicon

Ultraviolet radiation

Molecules

Luminescence

Signal detection

Refractive index

Optical testing

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