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 journalArticlepeer-review

18 Citations (Scopus)


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
Issue number1
Publication statusPublished - 2014 Apr

ASJC Scopus subject areas

  • General Chemistry
  • General Materials Science


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