Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope

Kim, Min Jun; McNally, Ben; Murata, Kazuyoshi; Meller, A.

doi:10.1088/0957-4484/18/20/205302

Cited by 160 publications

(177 citation statements)

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“…[235][236][237] In overview, nanopores as small as 1 nm in diameter and $10 nm long can be fabricated with some flexibility in fabrication method. Characterization of nanopores can be done using chargedparticle microscopes and related techniques such as electron tomography and EELS, 219,220,[238][239][240][241] or by much less instrumentally intensive (ionic) conductance-based approaches.…”

Section: Nanofluidic Sample Cellsmentioning

confidence: 99%

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

Dwyer

Harb

2017

Appl Spectrosc

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We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical natureof this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

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Section: Nanofluidic Sample Cellsmentioning

confidence: 99%

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

Dwyer

Harb

2017

Appl Spectrosc

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“…[70] Nanopores 4 to 8 nm in diameter were directly drilled using a JEOL 2010F . [70] TEM tomography was used to map the three-dimensional structure of these solid-state nanopores.…”

Section: Electron Beam Induced Sputteringmentioning

confidence: 99%

“…[70] Nanopores 4 to 8 nm in diameter were directly drilled using a JEOL 2010F . [70] TEM tomography was used to map the three-dimensional structure of these solid-state nanopores. It was observed that the sidewalls of the sputtered pores were angled (approximately 65° to the horizontal), attributed to the intensity distribution of the e-beam around its focal point.…”

Section: Electron Beam Induced Sputteringmentioning

confidence: 99%

“…Postdrilling, pores formed an 'hourglass' structure with pore width being represented by the width of the narrowest constriction. [70,71] Similarly, Heng et al used a focused convergent electron beam to form nanopores in ultra-thin 10 nm Si 3 N 4 membranes. The nanopore structure resembled a double cone structure with a cone angle of 10°.…”

Section: Electron Beam Induced Sputteringmentioning

confidence: 99%

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Solid-State Nanopore Sensors for Nucleic Acid Analysis

Venkatesan

Bashir

2011

Nanopores

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Nanopore DNA analysis is an emerging technique that involves electrophoretically driving DNA molecules through a nano-scale pore in solution and monitoring the corresponding change in ionic pore current. This versatile approach permits the label-free, amplification-free analysis of charged polymers (single stranded DNA, double stranded DNA and RNA) ranging in length from single nucleotides to kilobase long genomic DNA fragments with subnanometer resolution.Recent advances in nanopores suggest that this low-cost, highly scalable technology could lend itself to the development of third generation DNA sequencing technologies, promising rapid and reliable sequencing of the human diploid genome for under $1000.Here, we report the development of versatile, nano-manufactured Al 2 O 3 solid-state nanopores and nanopore arrays for rapid, label-free, single-molecule detection and analysis of DNA and protein. This nano-scale technology has proven to be reliable, affordable, and mass producible, and allows for integration with VLSI processes. A detailed characterization of nanopore performance in terms of electrical noise, mechanical robustness and materials analysis is provided, and the functionality of this technology in experimental DNA biophysics is explored.A framework for the application of this technology to medical diagnostics and sequencing is also presented. Specifically, studies involved the detection of DNA-protein complexes, a viable strategy in screening methylation patterns in panels of genes for early cancer detection, and the creation of lipid bilayer coated nanopore sensors, useful in creating hybrid biological/solid-state nanopores for DNA sequencing applications.The concept of a gated nanopore is also presented with preliminary results. The fabrication of this novel system has been enabled by the recent discovery of graphene, a highly versatile material with remarkable electrical and mechanical properties. Direct modulation of the nanopore conductance was observed through the application of potentials to the graphene gate.These exciting results suggest this technology could potentially be useful in slowing down or trapping a DNA molecule in the pore, thereby enabling solid-state nanopore sequencing.iii

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“…Studies using solid-state pores have recently begun to emerge, demonstrating the detection of double-stranded and ssDNA conformations (18 -26 ). Fabrication of solid-state nanopores enables the simultaneous threading of DNA through nanopore arrays (17,27 ), thus increasing throughput and allowing massive parallelism in DNA sequencing and analysis (see Fig. 4).…”

Section: Dna Translocation Through Nanoporesmentioning

confidence: 99%

Progress toward Ultrafast DNA Sequencing Using Solid-State Nanopores

Soni

Meller²

2007

Clinical Chemistry

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Background:Measurements of the ionic current flowing through nanometer-scale pores (nanopores) have been used to analyze single DNA and RNA molecules, with the ultimate goal of achieving ultrafast DNA sequencing. However, attempts at purely electronic measurements have not achieved the signal contrast required for single nucleotide differentiation. In this report we propose a novel method of optical detection of DNA sequence translocating through a nanopore. Methods: Each base of the target DNA sequence is 1st mapped onto a 2-unit code, 2 10-bp nucleotide sequence, by biochemical conversion into Designed DNA Polymers. These 2-unit codes are then hybridized to complementary, fluorescently labeled, and self-quenching molecular beacons. As the molecular beacons are sequentially unzipped during translocation through a <2-nm-wide nanopore, their fluorescent tags are unquenched and are detected by a custom-built dual-color total internal reflection fluorescence (TIRF) microscope. The 2-color optical signal is then correlated to the target DNA sequence. Results: A dual-color TIRFM microscope with singlemolecule resolution was constructed, and controlled fabrication of 1-dimensional and 2-dimensional arrays of solid-state nanopores was performed. A nanofluidic cell assembly was constructed for TIRF-based optical detection of voltage-driven DNA translocation through a nanopore. Conclusions: We present a novel nanopore-based DNA sequencing technique that uses an optical readout of DNA translocating unzipping through a nanopore. Our technique offers better single nucleotide differentiation in sequence readout, as well as the possibility of largescale parallelism using nanopore arrays.

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Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope

Cited by 160 publications

References 23 publications

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

Solid-State Nanopore Sensors for Nucleic Acid Analysis

Progress toward Ultrafast DNA Sequencing Using Solid-State Nanopores

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