DNA Translocation through Graphene Nanopores

Merchant, Christopher A.; Healy, Ken; Wanunu, Meni; Ray, Vishva; Peterman, Neil; Bartel, John; Fischbein, Michael D.; Venta, Kimberly; Luo, Zhengtang; Johnson, A. T. Charlie; Drndić, Marija

doi:10.1021/nl101046t

Cited by 873 publications

(941 citation statements)

References 48 publications

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“…The more populated component exhibits an average translocation duration of ≈22 ms which corresponds to ≈450 ns per bp. Interestingly the measured dwell time is 1.5 to ≈100 times longer than the reports for 2D (5 [15] -56 ns per bp [2] ), biological (30 ns per bp [29] ), and solid-state (40-300 ns per bp) nanopores. [30] Several observations suggest the presence of a strong interaction between DNA and the walls of the trench, which eventually slows down the translocation of molecules.…”

Section: Bionanotechnologycontrasting

confidence: 53%

Zero‐Depth Interfacial Nanopore Capillaries

et al. 2018

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Charged molecules can translocate through the nanopore. The instant passage of the molecule momentarily impacts the conductance by locally reducing the aperture size of the channel. The resulting variations of the ionic conductance depends on the local topology of the translocating molecule; particularly, portions of long chain molecules such as polymers, proteins or DNA mark the electronic readout with specific conductance blockade fingerprints, and ultimately allow for reconstructing the sequence of monomers composing the translocating strands. [10] Consequently, thinner pores, i.e., capillaries with shorter channels, are capable of resolving shorter portions of molecules, leading for instance toward highresolution sequencing devices. [1] Thus, the challenge toward high-resolution sequencing has driven the development of ultrashort channel nanopores. Historically, two major classes of nanopores, i.e., biological and solid state nanopores, have been considered. The thickness of these nanopores varies from a few nanometers, as for α-hemolysin biological nanopores, [11,12] up to tens of nanometers for solid-state nanopores. [13] A revolutionary breakthrough aiming at reducing the capillary length of nanopores was achieved by the introduction of 2D materials such as graphene, [14][15][16] hexagonal boron nitride, [17] and molybdenum disulfide. [18][19][20][21] Indeed, the monoatomic capillary length of 2D nanopores is expected to offer sequencing capabilities, [2] but has not been realized yet. Inferior mechanical stability is one of the downsides of thin membranes inherently limiting the sustainability of 2D nanopores. Moreover, the complex fabrication process, involving cleanroom facilities and electron beam lithography, [22][23][24] can be demanding to scale up to industrial production. The noise levels in such devices are also orders of magnitude higher than those for long capillary-based nanopores, thus hindering their application for sequencing. [25] To address these issues, we introduce the concept of interfacial nanopores, generated at the crossing of two trenches, as illustrated in Figure 1. Fundamentally, the cross-section of two 1D straight lines is a zero-dimensional entity defined as a point (Figure 1a). The addition of a second dimensionality implies the overlap of two components to become a surface (Figure 1b). Similarly, in a 3D space, the interface shared between two tangent rectangular parallelepipeds is a surface, hence mathematically 2D (Figure 1c). Unlike nanopores commonly fabricated in 2D materials-which notwithstanding still possess a finite thickness-the surface defined by the crossing parallelepipeds is strictly 2D and thus does not exhibit any thickness. A High-fidelity analysis of translocating biomolecules through nanopores demands shortening the nanocapillary length to a minimal value. Existing nanopores and capillaries, however, inherit a finite length from the parent membranes. Here, nanocapillaries of zero depth are formed by dissolving two superimposed and crossing metallic nanoro...

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Section: Bionanotechnologycontrasting

confidence: 53%

Zero‐Depth Interfacial Nanopore Capillaries

et al. 2018

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“…13 Apart from all these encouraging achievements, it is worth noting that the strong πÀπ interaction between graphene and DNA 14 leads to undesirable adsorption of DNA on graphene, which may hinder the DNA translocation through graphene nanopores. Some groups have exploited surface modification, 15 atomic layer deposition 5 and high pH and ionic strengths 4 to minimize surface interaction. The first two approaches ultimately increase the sensing length to few nanometers which is not desirable for single nucleotide resolution.…”

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confidence: 99%

Atomically Thin Molybdenum Disulfide Nanopores with High Sensitivity for DNA Translocation

et al. 2014

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Atomically thin nanopore membranes are considered to be a promising approach to achieve single base resolution with the ultimate aim of rapid and cheap DNA sequencing. Molybdenum disulfide (MoS2) is newly emerging as a material complementary to graphene due to its semiconductive nature and other interesting physical properties that can enable a wide range of potential sensing and nanoelectronics applications. Here, we demonstrate that monolayer or few-layer thick exfoliated MoS2 with subnanometer thickness can be transferred and suspended on a predesigned location on the 20 nm thick SiN x membranes. Nanopores in MoS2 are further sculpted with variable sizes using a transmission electron microscope (TEM) to drill through suspended portions of the MoS2 membrane. Various types of double-stranded (ds) DNA with different lengths and conformations are translocated through such a novel architecture, showing improved sensitivity (signal-to-noise ratio >10) compared to the conventional silicon nitride (SiN x ) nanopores with tens of nanometers thickness. Unlike graphene nanopores, no special surface treatment is needed to avoid hydrophobic interaction between DNA and the surface. Our results imply that MoS2 membranes with nanopore can complement graphene nanopore membranes and offer potentially better performance in transverse detection.

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“…Moreover, we believe that even smaller and thinner pores can be obtained with CIBS using lower energies and/or different sputter ions. Due to their very small effective thickness (comparable to single and multilayer graphene nanopores [19][20][21] ) and scalable fabrication, CIBS nanopores are ideal candidates for solid-state nanopore DNA sequencing systems.…”

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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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DNA Translocation through Graphene Nanopores

Cited by 873 publications

References 48 publications

Zero‐Depth Interfacial Nanopore Capillaries

Zero‐Depth Interfacial Nanopore Capillaries

Atomically Thin Molybdenum Disulfide Nanopores with High Sensitivity for DNA Translocation

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

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