High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore

Roshan, Kamyar Akbari; Tang, Zifan; Guan, Weihua

doi:10.1088/1361-6528/aaf48e

Cited by 25 publications

(38 citation statements)

References 60 publications

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“…An even smaller nanopore down to 1 nm in diameter can be fabricated by drilling a membrane with a focused-electron or helium-ion beam 30–34 . In addition, dielectric breakdown of a membrane has been widely utilized as a method of nanopore fabrication in recent years 35–61 because of its simplicity and inexpensiveness. With the application of a high constant voltage to a membrane and termination of the voltage when the current between the electrodes reaches a predetermined cut-off value, a nanopore can be created in a membrane.…”

Section: Introductionmentioning

confidence: 99%

Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules

Yanagi

Akahori

Takeda

2019

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For nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.

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Section: Introductionmentioning

confidence: 99%

Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules

Yanagi

Akahori

Takeda

2019

Sci Rep

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“…This phenomenon was previously observed in gel electrophoresis and was described by the Ogston−Morris− Rodbard−Chrambach model, in which molecule electrophoretic mobility has an exponential relationship with the obstacle concentration (μ ∝ − e C RNP ). 42,43 Hence, electrophoretic mobility of the reporters can be extracted by fitting an exponential curve to our experimental results (4) where μ 0 (1.73 × 10 −8 m 2 V −1 s −1 ) and β (0.025 nM −1 ) are the constants of the fitted exponential curve to the experimental results (SI Note S4). Experimentally observed events for negative and positive cases would follow the Poisson distribution with expected values of λ n and λ p , respectively.…”

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confidence: 99%

“…Solid-state nanopore sensors made from silicon nitride, − glass, − and graphene have shown great potential in detecting single molecules due to their unique label-free electronic sensing, single molecule sensitivity, and potential reusability. In typical nanopore experiments, charged biopolymers such as DNAs are electrophoretically driven through the nanoscale orifice, which temporarily blocks the passage of ions that leads to a dip in the current.…”

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confidence: 99%

Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN)

et al. 2020

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Nucleic acid detection methods are crucial for many fields such as pathogen detection and genotyping. Solid-state nanopore sensors represent a promising platform for nucleic acid detection due to its unique single molecule sensitivity and label-free electronic sensing. Here, we demonstrated the use of the glass nanopore for highly sensitive quantification of single-stranded circular DNAs (reporters), which could be degraded under the trans-cleavage activity of the target-specific CRISPR-Cas12a. We developed and optimized the Cas12a assay for HIV-1 analysis. We validated the concept of the solid-state CRISPR-Cas12a-assisted nanopores (SCAN) to specifically detect the HIV-1 DNAs. We showed that the glass nanopore sensor is effective in monitoring the cleavage activity of the target DNA-activated Cas12a. We developed a model to predict the total experimental time needed for making a statistically confident positive/negative call in a qualitative test. The SCAN concept combines the much-needed specificity and sensitivity into a single platform, and we anticipate that the SCAN would provide a compact, rapid, and low-cost method for nucleic acid detection at the point of care.

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“…The digital assays so far are predominated by physical partitioning and optical detection methods to generate the binary signal. Nanopore-based sensors − allow single molecules to be analyzed electronically without the need for labeling and partitioning. Conceptually, nanopore sensor represents an ideal single molecule counting device due to its unique features of label-free electronic sensing, single-molecule sensitivity, and potential reusability.…”

mentioning

confidence: 99%

Calibration-Free Nanopore Digital Counting of Single Molecules

2019

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Nanopore sensor conceptually represents an ideal single molecule counting device due to its unique partitioning-free, label-free electronic sensing. Existing theories and experiments have shown that sample concentration is proportional to the molecule translocation rate. However, a detailed nanopore geometry and size characterization or a calibration curve of concentration standards are often required for quantifying the unknown sample. In this work, we proposed and validated a calibration-free nanopore single molecule digital counting method for isolated molecule quantification. With the background ions as the in situ references, the molecule translocation rates can be normalized to the ion translocation rates (i.e., baseline current). This in situ reference alleviates the requirement for knowing the nanopore geometry and size or generating a calibration curve. In recognition of this effect, we developed a quantitative model for nanopore quantification without the need for prior knowledge of experimental conditions such as nanopore geometry, size, and applied voltage. This model was experimentally validated for different nanopores and DNA molecules with different sizes. We anticipate this calibration-free digital counting approach would provide a new avenue for nanopore-based molecule sensing.

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High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore

Abstract: High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore To cite this article: Kamyar Akbari Roshan et al 2019 Nanotechnology 30 095502 View the article online for updates and enhancements.

Cited by 25 publications

References 60 publications

Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules

Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules

Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN)

Calibration-Free Nanopore Digital Counting of Single Molecules

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