Optical detection of DNA translocation through silicon nanopore by ultraviolet light

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

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

In this paper, we propose a new optical detection scheme for nanopore-based DNA sequencing with high resolution towards eventual base identification. We use ultraviolet light for excitation of a fluorescent probe attached to DNA and a nanopore in the silicon membrane that has a significantly large refractive index and an extinction coefficient at ultraviolet wavelengths. In this study, numerical electromagnetic simulation revealed that the z-polarization component (perpendicular to the membrane plane) of the electric field was dominant near the nanopore and generated a large electric field gradient at the nanopore exit, typically with a decay length of 2 nm for a nanopore with diameter of 7 nm. The large extinction coefficient contributed to reduction in background noise coming from fluorophore-labeled DNA strands that remain behind the membrane (the cis side of the membrane). We observed a high signal-to-noise ratio of single DNA translocation events under the application of an electric field.

Original languageEnglish
Pages (from-to)53-56
Number of pages4
JournalApplied Physics A: Materials Science and Processing
Volume115
Issue number1
DOIs
Publication statusPublished - 2014

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Nanopores
Silicon
DNA
Membranes
Electric fields
Fluorophores
Fluorescent Dyes
Refractive index
Signal to noise ratio
Ultraviolet Rays
Polarization
Wavelength

ASJC Scopus subject areas

  • Materials Science(all)
  • Chemistry(all)

Cite this

Optical detection of DNA translocation through silicon nanopore by ultraviolet light. / Yamazaki, Hirohito; Kimura, Shinji; Tsukahara, Mutsumi; Esashika, Keiko; Saiki, Toshiharu.

In: Applied Physics A: Materials Science and Processing, Vol. 115, No. 1, 2014, p. 53-56.

Research output: Contribution to journalArticle

Yamazaki, Hirohito ; Kimura, Shinji ; Tsukahara, Mutsumi ; Esashika, Keiko ; Saiki, Toshiharu. / Optical detection of DNA translocation through silicon nanopore by ultraviolet light. In: Applied Physics A: Materials Science and Processing. 2014 ; Vol. 115, No. 1. pp. 53-56.
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