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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Liu HL, Ahmed SA, Jiang QC, Shen Q, Zhan K, Wang K. Gold Nanotriangle-Assembled Nanoporous Structures for Electric Field-Assisted Surface-Enhanced Raman Scattering Detection of Adenosine Triphosphate. ACS Sens 2023; 8:1280-1286. [PMID: 36920780 DOI: 10.1021/acssensors.2c02759] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A reliable, rapid, cost-effective, and simple method for the detection of biomolecules would greatly promote the research of analytical detection of single molecules. A nanopore-based analytical technique is promising for detecting biomolecules. Conventional electrochemical nanopores cannot distinguish biomolecules precisely because of their fast translocation speed and limited electrochemical information. Therefore, it is highly desirable to develop electrochemical surface-enhanced Raman scattering (SERS) nanopores to obtain multidimensional information. Herein, we designed and fabricated gold nanotriangle (AuNT)-assembled porous structures at the tip of a glass capillary using dithiol adenosine triphosphate (ATP) aptamers as cross-linking molecules. The AuNTs exhibited an edge length of 57.3 ± 6.2 nm and thickness of about 15 nm. The gold nanoporous structure (GPS) showed a strong ion rectification even at a high concentration of electrolyte (2 M) and a high SERS activity. Based on these designed structures, SERS and electrochemistry techniques were combined to control the rapid movement of ATP to the vicinity of the GPS by an applied potential of +1 V, where ATP was concentrated by ATP aptamers and the molecular signals were amplified by SERS. As a result, the GPS successfully detected ATP at a concentration as low as 10-7 M.
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Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
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Liu J, Xie X, Wang T, Chen H, Fu Y, Cheng X, Wu J, Li G, Liu C, Liimatainen H, Zheng Z, Wang X, Kaplan DL. Promotion of Wound Healing Using Nanoporous Silk Fibroin Sponges. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12696-12707. [PMID: 36855948 DOI: 10.1021/acsami.2c20274] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Wound dressings are important for wound repair. The morphology of the biomaterials used in these dressings, and in particular, the pore structure affects tissue regeneration by facilitating attachment and proliferation of cells due to the hierarchical multiscale, water absorbance, and nutrient transport. In the present study, silk fibroin (SF) sponges with walls containing nanopores (SFNS) were prepared from SF nanoparticles generated during the autoclaving of SF solutions, followed by leaching the SF nanoparticles from the freeze-dried sponges of SF. The nano/microporous structure, biofluid absorbance, and porosity of the SF sponges with and without nanopores were characterized. In vitro cell proliferation, in vivo biocompatibility, and wound healing were evaluated with the sponges. The results demonstrated that SFNS had significantly increased porosity and water permeability, as well as cell attachment and proliferation when compared with SF sponges without the nanopores (SFS). Wound dressings were assessed in a rat skin wound model, and SFNS was superior to SFS in accelerating wound healing, supported by vascularization, deposition of collagen, and increased epidermal thickness over 21 days. Hence, such a dressing material with a hierarchical multiscale pore structure could promote cell migration, vascularization, and tissue regeneration independently without adding any growth factor, which would offer a new strategy to design and engineer better-performed wound dressing.
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Wang Y, Zhu H, Xue Y, Yan P, Ouyang J. Microstructure Evolution with Rapid Thermal Annealing Time in (001)-Oriented Piezoelectric PZT Films Integrated on (111) Si. MATERIALS (BASEL, SWITZERLAND) 2023; 16:2068. [PMID: 36903182 PMCID: PMC10003855 DOI: 10.3390/ma16052068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In our recently published paper (Y.-Y. Wang et al., High performance LaNiO3-buffered, (001)-oriented PZT piezoelectric films integrated on (111) Si, Appl. Phys. Lett. 121, 182902, 2022), highly (001)-oriented PZT films with a large transverse piezoelectric coefficient e31,f prepared on (111) Si substrates were reported. This work is beneficial for the development of piezoelectric micro-electro-mechanical systems (Piezo-MEMS) because of (111) Si's isotropic mechanical properties and desirable etching characteristics. However, the underlying mechanism for the achievement of a high piezoelectric performance in these PZT films going through a rapid thermal annealing process has not been thoroughly analyzed. In this work, we present complete sets of data in microstructure (XRD, SEM and TEM) and electrical properties (ferroelectric, dielectric and piezoelectric) for these films with typical annealing times of 2, 5, 10 and 15 min. Through data analyses, we revealed competing effects in tuning the electrical properties of these PZT films, i.e., the removal of residual PbO and proliferation of nanopores with an increasing annealing time. The latter turned out to be the dominating factor for a deteriorated piezoelectric performance. Therefore, the PZT film with the shortest annealing time of 2 min showed the largest e31,f piezoelectric coefficient. Furthermore, the performance degradation occurred in the PZT film annealed for 10 min can be explained by a film morphology change, which involved not only the change in grain shape, but also the generation of a large amount of nanopores near its bottom interface.
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Chen K, Choudhary A, Sandler SE, Maffeo C, Ducati C, Aksimentiev A, Keyser UF. Super-Resolution Detection of DNA Nanostructures Using a Nanopore. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207434. [PMID: 36630969 DOI: 10.1002/adma.202207434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabeled single molecules in their native states. Here, label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometers is demonstrated. Using a narrow solid-state nanopore, the passage of a series of nanostructures attached to a freely translocating DNA molecule is detected, resolving individual nanostructures placed as close as 6 nm apart and with a surface-to-surface gap distance of only 2 nm. Such super-resolution ability is attributed to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. This work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping, and digital information storage independent of molecular motors.
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Ku CA, Chung CK. Advances in Humidity Nanosensors and Their Application: Review. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23042328. [PMID: 36850926 PMCID: PMC9960561 DOI: 10.3390/s23042328] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 05/27/2023]
Abstract
As the technology revolution and industrialization have flourished in the last few decades, the development of humidity nanosensors has become more important for the detection and control of humidity in the industry production line, food preservation, chemistry, agriculture and environmental monitoring. The new nanostructured materials and fabrication in nanosensors are linked to better sensor performance, especially for superior humidity sensing, following the intensive research into the design and synthesis of nanomaterials in the last few years. Various nanomaterials, such as ceramics, polymers, semiconductor and sulfide, carbon-based, triboelectrical nanogenerator (TENG), and MXene, have been studied for their potential ability to sense humidity with structures of nanowires, nanotubes, nanopores, and monolayers. These nanosensors have been synthesized via a wide range of processes, including solution synthesis, anodization, physical vapor deposition (PVD), or chemical vapor deposition (CVD). The sensing mechanism, process improvement and nanostructure modulation of different types of materials are mostly inexhaustible, but they are all inseparable from the goals of the effective response, high sensitivity and low response-recovery time of humidity sensors. In this review, we focus on the sensing mechanism of direct and indirect sensing, various fabrication methods, nanomaterial geometry and recent advances in humidity nanosensors. Various types of capacitive, resistive and optical humidity nanosensors are introduced, alongside illustration of the properties and nanostructures of various materials. The similarities and differences of the humidity-sensitive mechanisms of different types of materials are summarized. Applications such as IoT, and the environmental and human-body monitoring of nanosensors are the development trends for futures advancements.
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Chu Y, Zhang J, Zhang Y, Li Q, Jia Y, Dong X, Xiao J, Tao Y, Yang QH. Reconfiguring Hard Carbons with Emerging Sodium-ion Batteries: a Perspective. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2212186. [PMID: 36806260 DOI: 10.1002/adma.202212186] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Hard carbons, an important category of amorphous carbons, are non-graphitizable and are widely accepted as the most promising anode material for the emerging sodium-ion batteries (SIBs) because of their changeable low-potential charge/discharge plateaus. However, their microstructures are not fixed as layer-structured graphitic materials do and are difficult to accurately demonstrate. The successful use of hard carbons in SIBs revives the interests to give a clear picture of their complicated microstructures that are in close relevance to the sodium storage. In this review, we start by revisiting the past definitions and structural models of hard carbons, and then present our renewed understanding of their sodium storage mechanism, focusing especially on the critical low-potential plateaus. Three critical structural features are highlighted for hard carbons, namely crystallites, defects and nanopores, which are directly responsible for the presence of the low-potential plateaus and their reversible extension. The impact of these structural features upon the sodium storage is then deeply discussed and an ideal configuration, namely sieving carbons with tightened pore entrance and enlarged pore body, is finally proposed for superhigh sodium storage. We expect this review to offer a clear picture of hard carbons, and help realize a truly rational design of high-capacity carbon anodes engining the industrialization of SIBs, and more promisingly open up a window for exploring their possible new uses. This article is protected by copyright. All rights reserved.
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Andersson J, Järlebark J, KK S, Schaefer A, Hailes R, Palasingh C, Santoso B, Vu VT, Huang CJ, Westerlund F, Dahlin A. Polymer Brushes on Silica Nanostructures Prepared by Aminopropylsilatrane Click Chemistry: Superior Antifouling and Biofunctionality. ACS APPLIED MATERIALS & INTERFACES 2023; 15:10228-10239. [PMID: 36765467 PMCID: PMC9951205 DOI: 10.1021/acsami.2c21168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
In nanobiotechnology, the importance of controlling interactions between biological molecules and surfaces is paramount. In recent years, many devices based on nanostructured silicon materials have been presented, such as nanopores and nanochannels. However, there is still a clear lack of simple, reliable, and efficient protocols for preventing and controlling biomolecule adsorption in such structures. In this work, we show a simple method for passivation or selective biofunctionalization of silica, without the need for polymerization reactions or vapor-phase deposition. The surface is simply exposed stepwise to three different chemicals over the course of ∼1 h. First, the use of aminopropylsilatrane is used to create a monolayer of amines, yielding more uniform layers than conventional silanization protocols. Second, a cross-linker layer and click chemistry are used to make the surface reactive toward thiols. In the third step, thick and dense poly(ethylene glycol) brushes are prepared by a grafting-to approach. The modified surfaces are shown to be superior to existing options for silica modification, exhibiting ultralow fouling (a few ng/cm2) after exposure to crude serum. In addition, by including a fraction of biotinylated polymer end groups, the surface can be functionalized further. We show that avidin can be detected label-free from a serum solution with a selectivity (compared to nonspecific binding) of more than 98% without the need for a reference channel. Furthermore, we show that our method can passivate the interior of 150 nm × 100 nm nanochannels in silica, showing complete elimination of adsorption of a sticky fluorescent protein. Additionally, our method is shown to be compatible with modifications of solid-state nanopores in 20 nm thin silicon nitride membranes and reduces the noise in the ion current. We consider these findings highly important for the broad field of nanobiotechnology, and we believe that our method will be very useful for a great variety of surface-based sensors and analytical devices.
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Leong IW, Tsutsui M, Yokota K, Murayama S, Taniguchi M. Regulating Nonlinear Ion Transport through a Solid-State Pore by Partial Surface Coatings. ACS APPLIED MATERIALS & INTERFACES 2023; 15:6123-6132. [PMID: 36661232 DOI: 10.1021/acsami.2c19485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Using functional nanofluidic devices to manipulate ion transport allows us to explore the nanoscale development of blue energy harvesters and iontronic building blocks. Herein, we report on a method to alter the nonlinear ionic current through a pore by partial dielectric coatings. A variety of dielectric materials are examined on both the inner and outer surfaces of the channel with four different patterns of coated or uncoated surfaces. Through controlling the specific part of the surface charge, the pore can behave like a resistor, diode, and bipolar junction transistor. We use numerical simulations to find out the reason for the asymmetric ion transport in the pore and illustrate the relationship between specifically charged surfaces and electroosmotic flow. These findings help understand the role of the corresponding surface composition in ion transport, which provides a direct approach to modify the electroosmotic-flow-driven ionic current rectification in the channel-based device via dielectric coatings.
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Seo D, Kim D, Seo S, Park J, Kim T. Analyses of Pore-Size-Dependent Ionic Transport in Nanopores in the Presence of Concentration and Temperature Gradients. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2409-2418. [PMID: 36562122 DOI: 10.1021/acsami.2c17925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mass transport through nanopores occurs in various natural systems, including the human body. For example, ion transport across nerve cell membranes plays a significant role in neural signal transmission, which can be significantly affected by the electrolyte and temperature conditions. To better understand and control the underlying nanoscopic transport, it is necessary to develop multiphysical transport models as well as validate them using enhanced experimental methods for facile nanopore fabrication and precise nanoscale transport characterization. Here, we report a nanopore-integrated microfluidic platform to characterize ion transport in the presence of electrolyte and temperature gradients; we employ our previous self-assembled particle membrane (SAPM)-integrated microfluidic platform to produce various nanopores with different pore sizes. Subsequently, we quantify pore-size-dependent ionic transport by measuring the short circuit current (SCC) and open circuit voltage (OCV) across various nanopores by manipulating the electrolyte and temperature gradients. We establish three simple theoretical models that heavily depend on pore size, electrolyte concentration, and temperature and subsequently validate them with the experimental results. Finally, we anticipate that the results of this study would help clarify ion transport phenomena at low-temperature conditions, not only providing a fundamental understanding but also enabling practical applications of cryo-anesthesia in the near future.
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Tay N, Gan H, de Sousa FB, Shen L, Nóbrega DF, Peng C, Kilpatrick-Liverman L, Wang W, Lavender S, Pilch S, Han J. Improved mineralization of dental enamel by electrokinetic delivery of F - and Ca 2+ ions. Sci Rep 2023; 13:516. [PMID: 36627315 PMCID: PMC9832158 DOI: 10.1038/s41598-022-26423-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
This in vitro study evaluated the effects of the infiltration of F- and Ca2+ ions into human enamel by electrokinetic flow (EKF) on the enamel microhardness and F- content. Sound human enamel ground sections of unerupted third molars were infiltrated with de-ionized water by EKF and with F- ion by EKF respectively. All samples were submitted to two successive transverse acid-etch biopsies (etching times of 30 s and 20 min) to quantify F- ion infiltrated deep into enamel. Remarkably, sound enamel showed a large increase in microhardness (MH) after infiltration of NaF (p < 0.00001) and CaCl2 (p = 0.013) by EKF. Additionally, NaF-EKF increased the remineralization in the lesion body of artificial enamel caries lesions compared to controls (p < 0.01). With the enamel biopsy technique, at both etching times, more F- ions were found in the EKF-treated group than the control group (p << 0.05), and more fluoride was extracted from deeper biopsies in the NaF-EKF group. In conclusion, our results show that EKF treatment is superior in transporting Ca2+ and F- ions into sound enamel when compared to molecular diffusion, enhancing both the mineralization of sound enamel and the remineralization of artificial enamel caries.
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Vasileiadis A, Li Y, Lu Y, Hu YS, Wagemaker M. Role of Defects, Pores, and Interfaces in Deciphering the Alkali Metal Storage Mechanism in Hard Carbon. ACS APPLIED ENERGY MATERIALS 2023; 6:127-140. [PMID: 36644115 PMCID: PMC9832432 DOI: 10.1021/acsaem.2c02591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
There are several questions and controversies regarding the Na storage mechanism in hard carbon. This springs from the difficulty of probing the vast diversity of possible configurational environments for Na storage, including surface and defect sites, edges, pores, and intercalation morphologies. In the effort to explain the observed voltage profile, typically existing of a voltage slope section and a low-voltage plateau, several experimental and computational studies have provided a variety of contradicting results. This work employs density functional theory to thoroughly examine Na storage in hard carbon in combination with electrochemical experiments. Our calculation scheme disentangles the possible interactions by evaluating the enthalpies of formation, shedding light on the storage mechanisms. Parallel evaluation of the Li and K storage, and comparison with experiments, put forward a unified reaction mechanism for the three alkali metals. The results underline the importance of exposed metal surfaces and metal-carbon interfaces for the stability of the pore-filling mechanism responsible for the low-voltage plateau, in excellent agreement with the experimental voltage profiles. This generalized understanding provides insights into hard carbons as negative electrodes and their optimized properties.
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Fyta M. Functionalized electrodes embedded in nanopores: read-out enhancement? Chem Asian J 2023; 18:e202200916. [PMID: 36372991 PMCID: PMC10107472 DOI: 10.1002/asia.202200916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.
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Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing. Nat Commun 2022; 13:7939. [PMID: 36566265 PMCID: PMC9789962 DOI: 10.1038/s41467-022-35650-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.
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Katsiaounis S, Chourdakis N, Michail E, Fakis M, Polyzos I, Parthenios J, Papagelis K. Graphene nano-sieves by femtosecond laser irradiation. NANOTECHNOLOGY 2022; 34:105302. [PMID: 36542345 DOI: 10.1088/1361-6528/aca7cb] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The formation of nano-pores in graphene crystal structure is alternative way to engineer its electronic properties, chemical reactivity, and surface interactions, enabling applications in technological fields such as sensing, energy and separation. The past few years, nano-perforation of graphene sheets has been accomplished by a variety of different methods suffering mainly from poor scalability and cost efficiency issues. In this work, we introduce an experimental protocol to engineer nanometer scale pores in CVD graphene membranes under ambient conditions, using low power ultra-short laser pulses and overcoming the drawbacks of other perforation techniques. Using Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) we visualized and quantified the nanopore network while Raman spectroscopy is utilized to correlate the nano-perforated area with the nanotopographic imaging. We suggest that Raman imaging provides the identification of nanoporous area and, in combination with AFM, we provide solid evidence for the reproducibility of the method, since under these experimental conditions, nanopores of a certain size distribution are formed.
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Zhuang J, Ma L, Qiu Y. Characterization of the surface charge property and porosity of track-etched polymer membranes. Electrophoresis 2022; 43:2428-2435. [PMID: 36193776 DOI: 10.1002/elps.202200198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/20/2022] [Accepted: 09/25/2022] [Indexed: 12/13/2022]
Abstract
As an important property of porous membranes, the surface charge property determines many ionic behaviors of nanopores, such as ionic conductance and selectivity. Based on the dependence of electric double layers on bulk concentrations, ionic conductance through nanopores at high and low concentrations is governed by the bulk conductance and surface charge density, respectively. Here, through the investigation of ionic conductance inside track-etched single polyethylene terephthalate (PET) nanopores under various concentrations, the surface charge density of PET membranes is extracted as ∼-0.021 C/m2 at pH 10 over measurements with 40 PET nanopores. Simulations show that surface roughness can cause underestimation in surface charge density due to the inhibited electroosmotic flow. Then, the averaged pore size and porosity of track-etched multipore PET membranes are characterized by the developed ionic conductance method. Through coupled theoretical predictions in ionic conductance under high and low concentrations, the averaged pore size and porosity of porous membranes can be obtained simultaneously. Our method provides a simple and precise way to characterize the pore size and porosity of multipore membranes, especially for those with sub-100 nm pores and low porosities.
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Lamellar carbon nitride membrane for enhanced ion sieving and water desalination. Nat Commun 2022; 13:7339. [PMID: 36443321 PMCID: PMC9705542 DOI: 10.1038/s41467-022-35120-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Membrane-based water treatment processes offer possibility to alleviate the water scarcity dilemma in energy-efficient and sustainable ways, this has been exemplified in filtration membranes assembled from two-dimensional (2D) materials for water desalination purposes. Most representatives however tend to swell or disintegrate in a hydrated state, making precise ionic or molecular sieving a tough challenge. Here we report that the chemically robust 2D carbon nitride can be activated using aluminum polycations as pillars to modulate the interlayer spacing of the conjugated framework, the noncovalent interaction concomitantly affords a well-interlinked lamellar structure, to be carefully distinguished from random stacking patterns in conventional carbon nitride membranes. The conformally packed membrane is characterized by adaptive subnanochannel and structure integrity to allow excellent swelling resistance, and breaks permeability-selectivity trade-off limit in forward osmosis due to progressively regulated transport passage, achieving high salt rejection (>99.5%) and water flux (6 L m-2 h-1), along with tunable permeation behavior that enables water gating in acidic and alkaline environments. These findings position carbon nitride a rising building block to functionally expand the 2D membrane library for applications in water desalination and purification scenarios.
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70
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Bi S, Salanne M. Co-Ion Desorption as the Main Charging Mechanism in Metallic 1T-MoS 2 Supercapacitors. ACS NANO 2022; 16:18658-18666. [PMID: 36269844 DOI: 10.1021/acsnano.2c07272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metallic 1T-MoS2 is a promising electrode material for supercapacitor applications. Its layered structure allows the efficient intercalation of ions, leading to experimental volumetric capacitance as high as 140 F/cm3. Molecular dynamics could in principle be used to characterize its charging mechanism; however, unlike conventional nanoporous carbon, 1T-MoS2 is a multicomponent electrode. The Mo and S atoms have very different electronegativities so that 1T-MoS2 cannot be simulated accurately using the conventional constant potential method. In this work, we show that controlling the electrochemical potential of the atoms allows one to recover average partial charges for the elements in agreement with electronic structure calculations for the material at rest, without compromising the ability to simulate systems under an applied voltage. The simulations yield volumetric capacitances in agreement with experiments. We show that due to the large electronegativity of S, the co-ion desorption is the main charging mechanism at play during the charging process. This contrasts drastically with carbon materials for which ion exchange and counterion adsorption usually dominate. In the future, our method can be extended to the study of a wide range of families of 2D layered materials such as MXenes.
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A click chemistry amplified nanopore assay for ultrasensitive quantification of HIV-1 p24 antigen in clinical samples. Nat Commun 2022; 13:6852. [PMID: 36369146 PMCID: PMC9651128 DOI: 10.1038/s41467-022-34273-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Despite major advances in HIV testing, ultrasensitive detection of early infection remains challenging, especially for the viral capsid protein p24, which is an early virological biomarker of HIV-1 infection. Here, To improve p24 detection in patients missed by immunological tests that dominate the diagnostics market, we show a click chemistry amplified nanopore (CAN) assay for ultrasensitive quantitative detection. This strategy achieves a 20.8 fM (0.5 pg/ml) limit of detection for HIV-1 p24 antigen in human serum, demonstrating 20~100-fold higher analytical sensitivity than nanocluster-based immunoassays and clinically used enzyme-linked immunosorbent assay, respectively. Clinical validation of the CAN assay in a pilot cohort shows p24 quantification at ultra-low concentration range and correlation with CD4 count and viral load. We believe that this strategy can improve the utility of p24 antigen in detecting early infection and monitoring HIV progression and treatment efficacy, and also can be readily modified to detect other infectious diseases.
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Tsutsui M, Yokota K, He Y, Kawai T. Ionic Signal Amplification of DNA in a Nanopore. SMALL METHODS 2022; 6:e2200761. [PMID: 36196624 DOI: 10.1002/smtd.202200761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.
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Bandara YMNDY, Freedman KJ. Enhanced Signal to Noise Ratio Enables High Bandwidth Nanopore Recordings and Molecular Weight Profiling of Proteins. ACS NANO 2022; 16:14111-14120. [PMID: 36107037 DOI: 10.1021/acsnano.2c04046] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fast protein translocations often lead to bandwidth-limited amplitude-attenuated event signatures. In this study, we developed a protein- and electrolyte chemistry-centric pathway to construct a readily executable decision tree for the detection of non-attenuated protein translocations using conventional electronics. Each optimization encompasses increasing capture rate (CR), signal-to-noise ratio (SNR), and minimizing irreversible analyte clogging to collect >104 events/pipette spanning a host of electric fields. This was demonstrated using 11 proteins ranging from ∼12 kDa to ∼720 kDa. Moreover, both symmetric and asymmetric electrolyte conditions (cis and trans chamber electrolyte concentration ratios <> 1) were explored. As a result, asymmetric electrolyte conditions were favorable on the extreme ends of the size spectrum (i.e., larger, and smaller proteins) and while the remainder of proteins were best sensed under symmetric electrolyte conditions. Under these optimal conditions, only ≲10% of events were attenuated at 500 mV (≲ 5% for most proteins at 500 mV with only ≲1-5% of the population faster than ∼7 μs, which is the theoretical attenuation threshold for 100 kHz bandwidth). Finally, applied voltage (Vapp), peak current drop (ΔIp), electrolyte conductivity (K), and open-pore conductance (G0) were used to generate a linear relationship to evaluate the molecular weight of the protein (Mw) using plots of (dΔIp)/(dVapp) vs Mw/(G0/K).
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Cheng P, Espano J, Harkaway A, Naclerio AE, Moehring NK, Braeuninger-Weimer P, Kidambi PR. Nanoporous Atomically Thin Graphene Filters for Nanoscale Aerosols. ACS APPLIED MATERIALS & INTERFACES 2022; 14:41328-41336. [PMID: 36036893 DOI: 10.1021/acsami.2c10827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Filtering nanoparticulate aerosols from air streams is important for a wide range of personal protection equipment (PPE), including masks used for medical research, healthcare, law enforcement, first responders, and military applications. Conventional PPEs capable of filtering nanoparticles <300 nm are typically bulky and sacrifice breathability to maximize protection from exposure to harmful nanoparticulate aerosols including viruses ∼20-300 nm from air streams. Here, we show that nanopores introduced into centimeter-scale monolayer graphene supported on polycarbonate track-etched supports via a facile oxygen plasma etch can allow for filtration of aerosolized SiO2 nanoparticles of ∼5-20 nm from air steams while maintaining air permeance of ∼2.28-7.1 × 10-5 mol m-2 s-1 Pa-1. Furthermore, a systematic increase in oxygen plasma etch time allows for a tunable size-selective filtration of aerosolized nanoparticles. We demonstrate a new route to realize ultra-compact, lightweight, and conformal form-factor filters capable of blocking sub-20 nm aerosolized nanoparticles with particular relevance for biological/viral threat mitigation.
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Yuan Z, He G, Li SX, Misra RP, Strano MS, Blankschtein D. Gas Separations using Nanoporous Atomically Thin Membranes: Recent Theoretical, Simulation, and Experimental Advances. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201472. [PMID: 35389537 DOI: 10.1002/adma.202201472] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Porous graphene and other atomically thin 2D materials are regarded as highly promising membrane materials for high-performance gas separations due to their atomic thickness, large-scale synthesizability, excellent mechanical strength, and chemical stability. When these atomically thin materials contain a high areal density of gas-sieving nanoscale pores, they can exhibit both high gas permeances and high selectivities, which is beneficial for reducing the cost of gas-separation processes. Here, recent modeling and experimental advances in nanoporous atomically thin membranes for gas separations is discussed. The major challenges involved, including controlling pore size distributions, scaling up the membrane area, and matching theory with experimental results, are also highlighted. Finally, important future directions are proposed for real gas-separation applications of nanoporous atomically thin membranes.
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