Selective Sensing of Proteins Using Aptamer Functionalized Nanopore Extended Field‐Effect Transistors

Ren, Ren; Wang, Xiaoyi; Cai, Sheng-Lin; Zhang, Yanjun; Korchev, Yuri; Ivanov, Aleksandar P.; Edel, Joshua B.

doi:10.1002/smtd.202000356

Cited by 37 publications

(49 citation statements)

References 53 publications

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“…In this regard, the application of nanopores has not been limited to DNA sequencing and functionalized nanopores have been shown to be effective in high-speed single-molecule detection of proteins. FET-equipped, aptamer-functionalized nanopores have been used to detect human thrombin protein by Ren et al (2020). However, ensuing experimental investigations implied a different physics at work in these devices (Xie et al , 2012; Traversi et al , 2013) than that outlined above.…”

Section: Nanopore Sensing Methodsmentioning

confidence: 99%

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Nanopore-based DNA sequencing sensors and CMOS readout approaches

Habibi

Dawji

Ghafar-Zadeh

et al. 2021

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Purpose Nanopore-based molecular sensing and measurement, specifically DNA sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly. This evolution has been powered not only by improvements in the sensors themselves, but also in the assisting microelectronic CMOS readout circuitry closely interfaced to them. In this light, this paper aims to review established and emerging nanopore-based sensing modalities considered for DNA sequencing and CMOS microelectronic methods currently being used. Design/methodology/approach Readout and amplifier circuits, which are potentially appropriate for conditioning and conversion of nanopore signals for downstream processing, are studied. Furthermore, arrayed CMOS readout implementations are focused on and the relevant status of the nanopore sensor technology is reviewed as well. Findings Ion channel nanopore devices have unique properties compared with other electrochemical cells. Currently biological nanopores are the only variants reported which can be used for actual DNA sequencing. The translocation rate of DNA through such pores, the current range at which these cells operate on and the cell capacitance effect, all impose the necessity of using low-noise circuits in the process of signal detection. The requirement of using in-pixel low-noise circuits in turn tends to impose challenges in the implementation of large size arrays. Originality/value The study presents an overview on the readout circuits used for signal acquisition in electrochemical cell arrays and investigates the specific requirements necessary for implementation of nanopore-type electrochemical cell amplifiers and their associated readout electronics.

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Section: Nanopore Sensing Methodsmentioning

confidence: 99%

Section: Nanopore Sensing Methodsmentioning

confidence: 99%

Nanopore-based DNA sequencing sensors and CMOS readout approaches

Habibi

Dawji

Ghafar-Zadeh

et al. 2021

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show abstract

“…31 To overcome these limitations, several alternative nanopore sensing strategies have been proposed and demonstrated. One such technique relies on integrating nanoelectrode structures such as field-effect sensors 31,[67][68][69][70][71] and electron tunnelling nanogaps [72][73][74][75][76] with a nanopore. Changes in the current through these nanoelectrode structures occur as a result of analytes translocating through an integrated or nearby nanopore.…”

Section: Solid State Nanoporesmentioning

confidence: 99%

“…Moreover, it offers a route towards selective biomolecular detection. 71,150,151 It was recently demonstrated that adding NaClO to the solution during CBD resulted in a significant change in the nanopore surface charge even after the electrolyte was replaced. 152 For DNA translocation experiments, this change in the surface charge resulted in an increased event frequency and less pore clogging due to reduced electrostatic interactions between the pore walls and the translocating molecule.…”

Section: Advantages Of Controlled Breakdownmentioning

confidence: 99%

In situsolid-state nanopore fabrication

et al. 2021

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“… 4 An addition to the resistive pulse sensing method is a variety of sensing modalities that solid-state nanopores (SSNPs) can offer, including multicolor discrimination of labeled DNAs and polypeptides, 5 , 6 ultrasensitive detection of proteins using nanopore blockade sensors, 7 optical profiling based on local plasmonic effect, 8 and selective sensing with nanopore-extended field-effect transistors. 9 , 10 Compared to their biological counterparts, the remarkable versatility of SSNPs is due to their wide-range tunability in pore geometries and dimensions as well as mechanical robustness and stability. An added advantage with SSNPs is the compatibility of their fabrication with control electronics as well as optical measurement structures.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of DNA Clogging in Hafnium Oxide Nanopores

Zeng

Wen

et al. 2020

J. Phys. Chem. B

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Interfacing solid-state nanopores with biological systems has been exploited as a versatile analytical platform for analysis of individual biomolecules. Although clogging of solid-state nanopores due to nonspecific interactions between analytes and pore walls poses a persistent challenge in attaining the anticipated sensing efficacy, insufficient studies focus on elucidating the clogging dynamics. Herein, we investigate the DNA clogging behavior by passing double-stranded (ds) DNA molecules of different lengths through hafnium oxide(HfO 2 )-coated silicon (Si) nanopore arrays, at different bias voltages and electrolyte pH values. Employing stable and photoluminescent-free HfO 2 /Si nanopore arrays permits a parallelized visualization of DNA clogging with confocal fluorescence microscopy. We find that the probability of pore clogging increases with both DNA length and bias voltage. Two types of clogging are discerned: persistent and temporary. In the time-resolved analysis, temporary clogging events exhibit a shorter lifetime at higher bias voltage. Furthermore, we show that the surface charge density has a prominent effect on the clogging probability because of electrostatic attraction between the dsDNA and the HfO 2 pore walls. An analytical model based on examining the energy landscape along the DNA translocation trajectory is developed to qualitatively evaluate the DNA–pore interaction. Both experimental and theoretical results indicate that the occurrence of clogging is strongly dependent on the configuration of translocating DNA molecules and the electrostatic interaction between DNA and charged pore surface. These findings provide a detailed account of the DNA clogging phenomenon and are of practical interest for DNA sensing based on solid-state nanopores.

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Selective Sensing of Proteins Using Aptamer Functionalized Nanopore Extended Field‐Effect Transistors

Cited by 37 publications

References 53 publications

Nanopore-based DNA sequencing sensors and CMOS readout approaches

Nanopore-based DNA sequencing sensors and CMOS readout approaches

In situsolid-state nanopore fabrication

Dynamics of DNA Clogging in Hafnium Oxide Nanopores

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