A novel side-gated ultrathin-channel nanopore FET (SGNAFET) sensor for direct DNA sequencing

Yanagi, Itaru; Oura, Takeshi; Haga, T.; Ando, Masahiko; Yamamoto, Jiro; Mine, T.; Ishida, Tadao; Hatano, Toshiyuki; Akahori, Rena; Yokoi, Takeshi; Anazawa, Takashi; Goto, Yasushi

doi:10.1109/iedm.2013.6724629

2013 IEEE International Electron Devices Meeting 2013

DOI: 10.1109/iedm.2013.6724629

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A novel side-gated ultrathin-channel nanopore FET (SGNAFET) sensor for direct DNA sequencing

Itaru Yanagi

Takeshi Oura

T. Haga

et al.

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Cited by 9 publications

(8 citation statements)

References 16 publications

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“…Recently, “nanopore” technology has been attracting great attention and has become an important subject for study because of its potential to achieve label-free single-molecule DNA sequencing (i.e., direct DNA sequencing) with very high throughput at low cost 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 . In addition to this advantage, another advantage, specifically, the potential to read long DNA sequences (i.e., long-read DNA sequencing), is given by direct DNA sequencing utilising nanopores.…”

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confidence: 99%

“…One is “biological”, i.e., nanopores that are formed with biological molecules (“bio-nanopores”) 1 2 3 4 5 6 7 . The other is “solid-state”, i.e., nanopores that are formed with semiconductor-related materials (“solid-state nanopores”) 1 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 . The most well-known concept of DNA sequencing, common to both bio-nanopores and solid-state nanopores, detects changes in the ionic current through the nanopore during DNA translocation and identifies the four types of nucleotides from the changes in ionic current 1 2 3 4 5 6 7 12 13 14 15 16 17 18 19 20 21 22 23 24 26 27 .…”

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confidence: 99%

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Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection

Yanagi

Akahori

Hatano

et al. 2014

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To date, solid-state nanopores have been fabricated primarily through a focused-electronic beam via TEM. For mass production, however, a TEM beam is not suitable and an alternative fabrication method is required. Recently, a simple method for fabricating solid-state nanopores was reported by Kwok, H. et al. and used to fabricate a nanopore (down to 2 nm in size) in a membrane via dielectric breakdown. In the present study, to fabricate smaller nanopores stably—specifically with a diameter of 1 to 2 nm (which is an essential size for identifying each nucleotide)—via dielectric breakdown, a technique called “multilevel pulse-voltage injection” (MPVI) is proposed and evaluated. MPVI can generate nanopores with diameters of sub-1 nm in a 10-nm-thick Si3N4 membrane with a probability of 90%. The generated nanopores can be widened to the desired size (as high as 3 nm in diameter) with sub-nanometre precision, and the mean effective thickness of the fabricated nanopores was 3.7 nm.

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confidence: 99%

mentioning

confidence: 99%

Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection

Yanagi

Akahori

Hatano

et al. 2014

Sci Rep

Self Cite

133

155

View full text Add to dashboard Cite

show abstract

“…Compared with biological nanopores, solid-state nanopores have advantages in terms of robustness and possible large-scale integration. However, DNA sequencing with solid-state nanopores has not been demonstrated yet, although several ideas have been studied to achieve DNA sequencing based on solid-state nanopores 40 41 42 43 44 . The most famous DNA sequencing idea, common to both biological and solid-state nanopores, consists of detecting changes in the ionic current through a nanopore during the translocation of DNA and identifying the four types of nucleotides through these changes.…”

mentioning

confidence: 99%

Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process

Yanagi

Ishida

Fujisaki

et al. 2015

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To improve the spatial resolution of solid-state nanopores, thinning the membrane is a very important issue. The most commonly used membrane material for solid-state nanopores is silicon nitride (Si3N4). However, until now, stable wafer-scale fabrication of Si3N4 membranes with a thickness of less than 5 nm has not been reported, although a further reduction in thickness is desired to improve spatial resolution. In the present study, to fabricate thinner Si3N4 membranes with a thickness of less than 5 nm in a wafer, a new fabrication process that employs a polycrystalline-Si (poly-Si) sacrificial layer was developed. This process enables the stable fabrication of Si3N4 membranes with thicknesses of 3 nm. Nanopores were fabricated in the membrane using a transmission electron microscope (TEM) beam. Based on the relationship between the ionic current through the nanopores and their diameter, the effective thickness of the nanopores was estimated to range from 0.6 to 2.2 nm. Moreover, DNA translocation through the nanopores was observed.

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“…As another family of nanopores, biological pores naturally 1–4 nm in diameter, such as α-hemolysin (α-HL), Mycobacterium smegmatis protein A, Phi29 connector, Aerolysin, Cytolysin A, Outer Membrane Protein G, etc., have been explored for biosensing applications especially in DNA sequencing. In order to improve the sensing performance, efforts have been pursued with respect to novel device structures, such as field-effect transistor (FET)-nanopore devices, , pore-cavity–pore device, and zero-depth nanopore, and to new detection methods, such as plasmonic nanopore and scattering nanopore, as well as to unconventional signal pick-up circuits and data processing algorithms. − These attempts have an implicit focus on boosting the capability of single nanopores in sensing. In contrast, simultaneous translocation of a multitude of nanopores or nanochannels by a large number of nanoparticles for high-throughput and low-cost parallelized sensing has received much less attention.…”

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confidence: 99%

Group Behavior of Nanoparticles Translocating Multiple Nanopores

et al. 2018

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Nanopores have been implemented as nano-sensors for DNA sequencing, biomolecule inspection, chemical analysis, nanoparticle detection, etc. For high-throughput and parallelized measurement using nanopore arrays, individual addressability has been a crucial technological solution in order to enable scrutiny of signals generated at each and every nanopore. Here, an alternative pathway of employing arrayed nanopores to perform sensor functions is investigated by examining the group behavior of nanoparticles translocating multiple nanopores. As no individual addressability is required, fabrication of nanopore devices along with microfluidic cells and readout circuits can be greatly simplified.Experimentally, arrays of less than 10 pores are shown to be capable of analyzing translocating nanoparticles with a good signal-to-noise margin. According to theoretical predictions, more pores (than 10) per array can perform high-fidelity analysis if the noise level of the measurement system can be better controlled. More pores per array would also allow for faster measurement at lower concentration because of larger capture cross-sections for target nanoparticles. By experimentally varying the number of pores, the concentration of nanoparticles or the applied bias voltage across the nanopores, we have identified the basic characteristics of this multi-event process. By characterizing average pore current and associated standard deviation during translocation and by performing physical modeling and extensive numerical simulations, we have shown the possibility of determining the size and concentration of two kinds of translocating nanoparticles over four orders of magnitude in concentration. Hence, we have demonstrated the potential and versatility of the multiple-nanopore approach for high-throughput nanoparticle detection.

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A novel side-gated ultrathin-channel nanopore FET (SGNAFET) sensor for direct DNA sequencing

Cited by 9 publications

References 16 publications

Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection

Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection

Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process

Group Behavior of Nanoparticles Translocating Multiple Nanopores

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