Control of Shape and Material Composition of Solid-State Nanopores

Wu, Mingjie; Smeets, Ralph M. M.; Zandbergen, M.W.; Ziese, Ulrike; Krapf, Diego; Batson, Philip E.; Dekker, Nynke H.; Dekker, Cees; Zandbergen, H.W.

doi:10.1021/nl803613s

Cited by 95 publications

(95 citation statements)

References 17 publications

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“…Thickness profiles of solid-state nanopores have been previously estimated using energy filtered transmission electron microscopy (EFTEM) maps and electron tomography, 7,8 but these methods are not well suited for our study. EFTEM maps rely on a calculated mean free path, which is subject to error for materials that are not well-characterized, and tomography requires extensive electron exposure of the nanopore, which we have found to damage thin nanopores and modify their geometry.…”

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confidence: 99%

Nanometer-thin solid-state nanopores by cold ion beam sculpting

Kuan

Golovchenko

2012

Applied Physics Letters

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Recent work on protein nanopores indicates that single molecule characterization (including DNA sequencing) is possible when the length of the nanopore constriction is about a nanometer. Solid-state nanopores offer advantages in stability and tunability, but a scalable method for creating nanometer-thin solid-state pores has yet to be demonstrated. Here we demonstrate that solid-state nanopores with nanometer-thin constrictions can be produced by "cold ion beam sculpting," an original method that is broadly applicable to many materials, is easily scalable, and requires only modest instrumentation. Initially, "ion beam sculpting" was used to fabricate solid-state nanopores capable of detecting single DNA molecules. 1 That original process took advantage of the surprising observation that at room temperature a low energy argon ion beam can shrink large prefabricated pores in thin silicon nitride (SiN) and oxide membranes to single digit nanometer diameters, creating an accumulated volcano-like mound of material that defines the nanopore. 2 However, the material constituency and precise internal geometry (including thickness) of pores produced by this additive process are difficult to control and are not well characterized or understood. Ion beam sculpting has been semi-quantitatively described with an adatom diffusion model in which an ion beam induced electric field near the pore causes accumulation of mobile surface adatoms created by the ion beam. 3 The distance from the pore edge X m within which adatoms are more likely to reach the pore than be annihilated by the ion beam or trapped at local surface defects is characterized by 4where l trap is the average distance between surface defects, r is the cross section for adatom annihilation by an incident ion, D is the surface diffusivity of adatoms, and F is the ion flux. At low temperatures, the surface diffusivity D can be reduced to the point that X m approaches zero and prefabricated SiN pores open instead of close under ion beam exposure. 1,4 In this work we show that in the low temperature limit, surface diffusion is almost completely suppressed and removal of material by sputtering dominates pore formation, allowing the fabrication of very thin nanopores. This cold ion beam sculpting (CIBS) method does not require preexisting pores and eliminates the "volcano phenomenon."A focused ion beam (FIB) machine (FEI Micrion, 50 keV Ga) was used to mill a bowl-shaped ($100 nm diameter) cavity on one side of a $250 nm thick free-standing silicon nitride (SiN) membrane. Then, in an ion sculpting apparatus described elsewhere 5 (Fig.

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confidence: 99%

Nanometer-thin solid-state nanopores by cold ion beam sculpting

Kuan

Golovchenko

2012

Applied Physics Letters

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“…One such protein-DNA system will be presented in the next chapter. [78,116] Note that Si rich particles were also observed in the pore vicinity in SiO 2 /SiN/SiO 2 systems, attributed to the preferential sputtering of O and N. It is therefore plausible that the material composition of our graphene-Al 2 O 3 nanopore is a combination of C, Al, and O fused together. The pH response, isoelectric point and surface charge density of this melded material system will likely deviate significantly from bulk ALD Al 2 O 3 or pure graphene response due to changes in bond lengths, co-ordinations and material composition in the sputtered system.…”

Section: Detection Of Estrogen Receptor α and Ere Complexesmentioning

confidence: 89%

“…[84,115] While these surface chemistries have been characterized in detail on planar surfaces, questions still remain as to the exact packing density, molecular orientation and thickness of SAM's in a highly confined environment that is a nanopore. In addition, nanopores formed via TEM decompositional sputtering processes typically exhibit high surface roughness, high surface curvature and a non-stoichiometric material composition due to selective material sputtering, as observed in SiO 2 and Si 3 N 4 nanopores, [78,116] further complicating the nanopore functionalization process. In these cases it is vital to thoroughly oxidize the surface through an extensive O 2 plasma treatment or a liquid based treatment in 1:3 H 2 O 2 :H 2 SO 4 .…”

Section: Hybrid Biological/solid-state Nanoporesmentioning

confidence: 99%

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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“…[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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Control of Shape and Material Composition of Solid-State Nanopores

Cited by 95 publications

References 17 publications

Nanometer-thin solid-state nanopores by cold ion beam sculpting

Nanometer-thin solid-state nanopores by cold ion beam sculpting

Solid-State Nanopore Sensors for Nucleic Acid Analysis

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

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