Ultra-thin, high-lifetime silicon nitride nanopore membranes for biosensing

Dutt, Shankar; Karawdeniya, Buddini I.; Bandara, Nuwan; Afrin, Nahid; Kluth, Patrick

doi:10.1016/j.bpj.2022.11.978

Cited by 6 publications

(9 citation statements)

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“…Nanopore Fabrication: Free standing, ∼7 nm thick silicon nitride membranes with a 100 nm thick silicon dioxide underlayer of size 40 μm x 40 μm on a 300 μm thick silicon frame were fabricated as discussed previously. [47] The membranes were placed between two custom built PMMA half cells, with reservoirs containing a 1 M KCl electrolyte solution buffered to a pH of 7. A Keithely 2450 sourcemeter was used to apply an electric field <1 V nm −1 across the membrane, which was stopped as soon as a rapid surge in current was observed, indicating the creation of a nanopore.…”

Section: Methodsmentioning

confidence: 99%

High Accuracy Protein Identification: Fusion of Solid‐State Nanopore Sensing and Machine Learning

Dutt,

Shao,

Karawdeniya

et al. 2023

Small Methods

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Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label‐free solid‐state nanopore sensing is a versatile technique for sensing and analyzing biomolecules such as proteins at single‐molecule level. While molecular‐level information on size, shape, and charge of proteins can be assessed by nanopores, the identification of proteins with comparable sizes remains a challenge. Here, solid‐state nanopore sensing is combined with machine learning to address this challenge. The translocations of four similarly sized proteins is assessed using amplifiers with bandwidths (BWs) of 100 kHz and 10 MHz, the highest bandwidth reported for protein sensing, using nanopores fabricated in <10 nm thick silicon nitride membranes. F‐values of up to 65.9% and 83.2% (without clustering of the protein signals) are achieved with 100 kHz and 10 MHz BW measurements, respectively, for identification of the four proteins. The accuracy of protein identification is further enhanced by classifying the signals into different clusters based on signal attributes, with F‐value and specificity of up to 88.7% and 96.4%, respectively, for combinations of four proteins. The combined use of high bandwidth instruments, advanced clustering and machine learning methods allows label‐free identification of proteins with high accuracy.

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Section: Methodsmentioning

confidence: 99%

High Accuracy Protein Identification: Fusion of Solid‐State Nanopore Sensing and Machine Learning

Dutt,

Shao,

Karawdeniya

et al. 2023

Small Methods

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“…Nanopores were fabricated using the CBD method with estimated pore diameters of ∼2 nm. The surface charge density was determined by surveying the open pore conductance with changing pH and salt concentrations [54] …”

Section: Fabrication Methods Of Nanopore Arraysmentioning

confidence: 99%

“…The surface charge density was determined by surveying the open pore conductance with changing pH and salt concentrations. [54] The ECR method utilizes the same experimental procedures as the CBD method. The term ECR was first coined in 2015 when a large electric field was used to create nanopores in a MoS 2 film suspended above an aperture in a SiNx membrane.…”

Section: In Situ Methods (Cbd Ecr and La-cbd)mentioning

confidence: 99%

Array of Nanopore Sensors Detect Nanoscale Biomolecules by Nucleic Acid Analysis

Song

et al. 2023

ChemistrySelect

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As a powerful technology, Array nanomaterials technology is widely used in the detection of biomolecules because the analytes of interest are detected and analyzed within a nanovolume. The solid-state nanopore array has a vast diversity of platforms and applications, such as improving the detection sensitivity of single molecules, achieving the goals of target detection, elevating the performance of anti-interference and realizing high-throughput and real-time measurement. It has made breakthrough progress in the qualitative and quantitative detection of various targets. However, no single review can cover the entire landscape of published work in the field. This article does not aim to cite all articles relating to solid-state nanopore arrays, but rather aims to highlight recent, select developments that will hopefully benefit new and seasoned scientists alike. Initially, the structure fabrication methods used in solid-state nanopore detection that apply transmission electron microscopes (TEMs), chemical etching, focused ion/ electron beams (FIB/FEB), will be introduced. Then, the next section is devoted to highlighting various surface functionalization methods. Finally, this review focuses on arrayed nanopores, as nucleic acid sensing technologies have great potential applications in the detection and measurement of DNA, RNA, protein and other analytes (such as new agents, bacteria, viruses, nanoparticles and polysaccharides).

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“…28 The default pore diameter and length were 10 and 50 nm, respectively. 14,30,33,34 The system temperature was maintained at 298 K, and the dielectric constant of water was set to 80. Because KCl solutions are commonly applied in biosensing based on nanopores, [35][36][37] KCl solutions varying from 10 to 500 mM in concentration were chosen in the simulations, of which 100 mM was the default concentration.…”

Section: Simulation Detailsmentioning

confidence: 99%

Modulation mechanism of ionic transport through short nanopores by charged exterior surfaces

Ma,

Liu,

Man

et al. 2023

Nanoscale

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Ultra-thin, high-lifetime silicon nitride nanopore membranes for biosensing

Cited by 6 publications

References 0 publications

High Accuracy Protein Identification: Fusion of Solid‐State Nanopore Sensing and Machine Learning

High Accuracy Protein Identification: Fusion of Solid‐State Nanopore Sensing and Machine Learning

Array of Nanopore Sensors Detect Nanoscale Biomolecules by Nucleic Acid Analysis

Modulation mechanism of ionic transport through short nanopores by charged exterior surfaces

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