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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish
Title of host publicationNanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI
PublisherSPIE
ISBN (Print)9780819498670
DOIs
Publication statusPublished - 2014 Jan 1
EventNanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI - San Francisco, CA, United States
Duration: 2014 Feb 32014 Feb 6

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume8954
ISSN (Print)1605-7422

Other

OtherNanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI
CountryUnited States
CitySan Francisco, CA
Period14/2/314/2/6

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Keywords

  • DNA sequencing
  • nano-photonics
  • nanopore
  • near-field optics
  • ultraviolet light

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging

Cite this

Yamazaki, H., Kimura, S., Tsukahara, M., Ito, S., Esashika, K., & Saiki, T. (2014). Highly sensitive measurement of single DNA translocation through an ultraviolet light spot on silicon nanopore. In Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XI [895407] (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 8954). SPIE. https://doi.org/10.1117/12.2036648