1
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Young TW, Kappler MP, Call ED, Brown QJ, Jacobson SC. Integrated In-Plane Nanofluidic Devices for Resistive-Pulse Sensing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:221-242. [PMID: 38608295 DOI: 10.1146/annurev-anchem-061622-030223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Single-particle (or digital) measurements enhance sensitivity (10- to 100-fold improvement) and uncover heterogeneity within a population (one event in 100 to 10,000). Many biological systems are significantly influenced by rare or infrequent events, and determining what species is present, in what quantity, and the role of that species is critically important to unraveling many questions. To develop these measurement systems, resistive-pulse sensing is used as a label-free, single-particle detection technique and can be combined with a range of functional elements, e.g., mixers, reactors, filters, separators, and pores. Virtually, any two-dimensional layout of the micro- and nanofluidic conduits can be envisioned, designed, and fabricated in the plane of the device. Multiple nanopores in series lead to higher-precision measurements of particle size, shape, and charge, and reactions coupled directly with the particle-size measurements improve temporal response. Moreover, other detection techniques, e.g., fluorescence, are highly compatible with the in-plane format. These integrated in-plane nanofluidic devices expand the toolbox of what is possible with single-particle measurements.
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Affiliation(s)
- Tanner W Young
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Michael P Kappler
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Ethan D Call
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - Quintin J Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
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2
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Feng Y, Xu S, Zheng J, Huang L, Ye T, Wang G, Jiang Y, Liu N. Crown-Ether Crystal Channel Membranes with Subnanometer Pores for Selective Na + Transport. ACS APPLIED MATERIALS & INTERFACES 2024; 16:26817-26823. [PMID: 38727564 DOI: 10.1021/acsami.4c05613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Emulating biological sodium ion channels to achieve high selectivity and rapid Na+ transport is important for water desalination, energy conversion, and separation processes. However, the development of artificial ion channels, especially multichannels, to achieve high ion selectivity, remains a challenge. In this work, we demonstrate the fabrication of ion channel membranes utilizing crown-ether crystals (DA18C6-nitrate crystals), which feature extremely consistent subnanometer pores. The polyethylene terephthalate (PET) membranes were initially subjected to amination, followed by the in situ growth of DA18C6-nitrate crystals to establish ordered multichannels aimed at facilitating selective Na+ conductance. These channels allow rapid Na+ transport while inhibiting the migration of other ions (K+ and Ca2+). The Na+ transport rate was 2.15 mol m-2 h-1, resulting in the Na+/K+ and Na+/Ca2+ selectivity ratios of 6.53 and 12.56, respectively. Due to the immobilization of the crown-ether ring, when the size of the transmembrane ion exceeded that of the crown-ether ring's cavity, the ions had to undergo a dehydration process to pass through the channel. This resulted in the ions encountering a higher energy barrier upon entering the channel, making it more difficult for them to permeate. However, the size of Na+ was compatible with the cavity of the crown-ether ring and was able to displace the hydrated layer effectively, facilitating selective Na+ translocation. In summary, this research offers a promising approach for the future development of functionalized ion channels and efficient membrane materials tailored for high-performance Na+ separation.
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Affiliation(s)
- Yueyue Feng
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Shiwei Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Liying Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Tingyan Ye
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Guofeng Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P.R. China
- Institute of New Materials and Industry Technology, Wenzhou University, Wenzhou 325000, P.R China
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3
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Lin X, Chen H, Wu G, Zhao J, Zhang Y, Sha J, Si W. Selective Capture and Manipulation of DNA through Double Charged Nanopores. J Phys Chem Lett 2024:5120-5129. [PMID: 38709198 DOI: 10.1021/acs.jpclett.4c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
In the past few decades, nanometer-scale pores have been employed as powerful tools for sensing biological molecules. Owing to its unique structure and properties, solid-state nanopores provide interesting opportunities for the development of DNA sequencing technology. Controlling DNA translocation in nanopores is an important means of improving the accuracy of sequencing. Here we present a proof of principle study of accelerating DNA captured across targeted graphene nanopores using surface charge density and find the intrinsic mechanism of the combination of electroosmotic flow induced by charges of nanopore and electrostatic attraction/repulsion between the nanopore and ssDNA. The theoretical study performed here provides a new means for controlling DNA transport dynamics and makes better and cheaper application of graphene in molecular sequencing.
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Affiliation(s)
- Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Haonan Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Jiajia Zhao
- Department of Pharmacology, Key Laboratory of Neuropsychiatric Diseases, China Pharmaceutical University, Nanjing 211198, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
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4
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Liu T, He X, Zhao J, Shi L, Zhou T, Wen L. Ion transport properties in the pH-dependent bipolar nanochannels. Electrophoresis 2023; 44:1847-1858. [PMID: 37401641 DOI: 10.1002/elps.202300073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/05/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
In recent years, researchers have made significant strides in understanding the ion transport characteristics of nanochannels, resulting in the development of various materials, modifications, and shapes of nano ion channel membranes. The aim is to create a nanochannel membrane with optimal ion transport properties and high stability by adjusting factors, such as channel size, surface charge, and wettability. However, during the nanochannel film fabrication process, controlling the geometric structures of nanochannels can be challenging. Therefore, exploring the stability of nanochannel performance under different geometric structures has become an essential aspect of nanochannel design. This article focuses on the study of cylindrical nanochannel structures, which are categorized based on the different methods for generating bipolar surface charges on the channel's inner surface, either through pH gradient effects or different material types. Through these two approaches, the study designed and analyzed the stability of ion transport characteristics in two nanochannel models under varying geometric structures. Our findings indicate that nanochannels with bipolar properties generated through pH gradients demonstrate more stable ion selection, whereas nanochannels with bipolar properties generated through different materials show stronger stability in ion rectification. This conclusion provides a theoretical foundation for future nanochannel designs.
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Affiliation(s)
- Tao Liu
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Xiaohan He
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Juncheng Zhao
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Liuyong Shi
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Teng Zhou
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Liping Wen
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, P. R. China
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5
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Kim JS, Kwon SY, Lee JY, Kim SD, Kim DY, Kim H, Jang N, Wang J, Han M, Kong SH. High-throughput multi-gate microfluidic resistive pulse sensing for biological nanoparticle detection. LAB ON A CHIP 2023; 23:1945-1953. [PMID: 36897079 DOI: 10.1039/d2lc01064j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A microfluidic resistive pulse sensing technique offers a simple method for detecting and analysing microparticles in various fields, yet it has challenges such as the noise during detection and low throughput as the signal obtained from a small single sensing aperture and particle position is nonuniform. This study presents a microfluidic chip with multiple detection gates in the main channel to enhance the throughput while maintaining a simple operational system. A hydrodynamic sheathless particle focusing on a detection gate by modulation of the channel structure and measurement circuit with a reference gate to minimize the noise during detection is used for detecting resistive pulses. The proposed microfluidic chip can analyse the physical properties of 200 nm polystyrene particles and exosomes from MDA-MB-231 with high sensitivity with an error of <10% and high-throughput screening of more than 200 000 exosomes per seconds. The proposed microfluidic chip can analyse the physical properties with high sensitivity, so that it can be potentially used for exosome detection in biological and in vitro clinical applications.
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Affiliation(s)
- June Soo Kim
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Soon Yeol Kwon
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Jae Yong Lee
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Seung Deok Kim
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Da Ye Kim
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Hyunjun Kim
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Noah Jang
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Jiajie Wang
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Maeum Han
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
| | - Seong Ho Kong
- School of Electronic and Electrical Engineering, Kyungpook National University, 41566, Daegu, Republic of Korea.
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6
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Cheng Y, Xia C, Garalleh HA, Garaleh M, Lan Chi NT, Brindhadevi K. A review on optimistic development of polymeric nanocomposite membrane on environmental remediation. CHEMOSPHERE 2023; 315:137706. [PMID: 36592836 DOI: 10.1016/j.chemosphere.2022.137706] [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: 10/26/2022] [Revised: 12/13/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Current health and environmental concerns about the abundance and drawbacks of municipal wastewater as well as industrial effluent have prompted the development of novel and innovative treatment processes. A global shortage of clean water poses significant challenges to the survival of all life forms. For the removal of both biodegradable and non-biodegradable harmful wastes/pollutants from water, sophisticated wastewater treatment technologies are required. Polymer membrane technology is critical to overcoming this major challenge. Polymer matrix-based nanocomposite membranes are among the most popular in polymer membrane technology in terms of convenience. These membranes and their major components are environmentally friendly, energy efficient, cost effective, operationally versatile, and feasible. This review provides an overview of the drawbacks as well as promising developments in polymer membrane and nanocomposite membranes for environmental remediation, with a focus on wastewater treatment. Additionally, the advantages of nanocomposite membranes such as stability, antimicrobial properties, and adsorption processes have been discussed. The goal of this review was to summarize the remediation of harmful pollutants from water and wastewater/effluent using polymer matrix-based nanocomposite membrane technology, and to highlight its shortcomings and future prospects.
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Affiliation(s)
- Yueqin Cheng
- Nanjing Station of Quality Protection in Cultivated Land, Nanjing, 210036, China
| | - Changlei Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Hakim Al Garalleh
- Department of Mathematical Science, College of Engineering, University of Business and Technology-Dahban, Jeddah, 21361, Saudi Arabia
| | - Mazen Garaleh
- Department of Mathematical Science, College of Engineering, University of Business and Technology-Dahban, Jeddah, 21361, Saudi Arabia; Department of Applied Chemistry, Faculty of Science, Tafila Technical University, Tafila, 66141, Jordan
| | - Nguyen Thuy Lan Chi
- School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Kathirvel Brindhadevi
- Computational Engineering and Design Research Group, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam.
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7
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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8
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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9
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Zhang M, Harms ZD, Greibe T, Starr CA, Zlotnick A, Jacobson SC. In-Plane, In-Series Nanopores with Circular Cross Sections for Resistive-Pulse Sensing. ACS NANO 2022; 16:7352-7360. [PMID: 35500295 PMCID: PMC9626396 DOI: 10.1021/acsnano.1c08680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Resistive-pulse sensing with solid-state nanopores is a sensitive, label-free technique for analyzing single molecules in solution. To add functionality to resistive-pulse measurements, direct coupling of the nanopores to other pores and nanoscale fluidic elements, e.g., reactors, separators, and filters, in the same device is an important next step. One approach is monolithic fabrication of the fluidic elements in the plane of the substrate, but methods to generate pores with circular cross sections are needed to improve sensing performance with in-plane devices. Here, we report a fabrication method that directly patterns nanopores with circular cross sections in series and in plane with the substrate. A focused ion beam instrument is used to mill a lamella in a nanochannel and, subsequently, bore a nanopore through the lamella. The diameter and geometry of the nanopore are controlled by the current and dose of the ion beam and by the tilt angle and thickness of the lamella. We fabricated devices with vertical and tilted lamellae and nanopores with diameters from 40 to 90 nm in cylindrical and conical geometries. To test device performance, we conducted resistive-pulse measurements of hepatitis B virus capsids. Current pulses from T = 3 capsids (∼31 nm diameter) and T = 4 capsids (∼35 nm diameter) were well resolved and exhibited relative pulse amplitudes (Δi/i) up to 5 times higher than data obtained on nanopores with rectangular cross sections. For smaller pore diameters (<45 nm), which approach the diameters of the capsids, a dramatic increase in the pulse amplitude was observed for both T = 3 and T = 4 capsids. Two and three pores fabricated in series further improved the resolution between the relative pulse amplitude distributions for the T = 3 and T = 4 capsids by up to 2-fold.
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Affiliation(s)
- Mi Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States of America
| | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States of America
| | - Tine Greibe
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States of America
| | - Caleb A. Starr
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7003, United States of America
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7003, United States of America
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States of America
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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Bakouei M, Abdorahimzadeh S, Taghipoor M. Effects of cone angle and length of nanopores on the resistive pulse quality. Phys Chem Chem Phys 2020; 22:25306-25314. [PMID: 33140790 DOI: 10.1039/d0cp04728g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Resistive pulse sensing (RPS) has proved to be a viable method for the detection and characterization of micro and nano particles. Modern fabrication methods have introduced different nanopore geometries for resistive pulse sensors. In this paper, we have numerically studied the effects of membrane thickness and the pore's cone angle, as the main geometrical parameters, on the sensing performance of the nanopores used for nanoparticle detection in the resistive pulse sensing method. To compare the sensing performance, three resistive pulse quality parameters were investigated - sensitivity, pulse duration and pulse amplitude. The thorough investigation on the relations between the geometrical parameters and the pulse quality parameters produced several interesting results, which were categorized and summarized for different nanopore structures (as different nanopore platforms) enabling the readers to more effectively compare them with one another. The results revealed that large cone angle and low aspect ratio nanopores have higher pulse amplitude and sensitivity, but their low duration could be a challenge in the process of detecting the resistive pulse. In addition, our results show small variation in sensitivity and duration of large cone angle nanopores with respect to pore length change, which is explained using the effective length concept and the definition of electric field strength and length. The findings of the present work can be used in practical applications where choosing the optimal pore geometry is of crucial significance. Furthermore, the results provide several possible ways to improve the resistive pulse quality for better sensing performance.
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Affiliation(s)
- Mostafa Bakouei
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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12
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Kumawat RL, Pathak B. Functionalized carbon nanotube electrodes for controlled DNA sequencing. NANOSCALE ADVANCES 2020; 2:4041-4050. [PMID: 36132799 PMCID: PMC9417824 DOI: 10.1039/d0na00241k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/14/2020] [Indexed: 06/14/2023]
Abstract
In the last decade, solid-state nanopores/nanogaps have attracted significant attention in the rapid detection of DNA nucleotides. However, reducing the noise through controlled translocation of the DNA nucleobases is a central issue for the development of nanogap/nanopore-based DNA sequencing to achieve single-nucleobase resolution. Furthermore, the high reactivity of the graphene pores/gaps causes clogging of the pore/gap, leading to the blockage of the pores/gaps, sticking, and irreversible pore closure. To address the prospective of functionalization of the carbon nanostructure and for accomplishing this objective, herein, we have studied the performance of functionalized closed-end cap armchair carbon nanotube (CNT) nanogap-embedded electrodes, which can improve the coupling through non-bonding electrons and may provide the possibility of N/O-H⋯π interactions with the nucleotides, as single-stranded DNA is transmigrated across the electrode. We have investigated the effect of functionalizing the closed-end cap CNT (6,6) electrodes with purine (adenine, guanine) and pyrimidine (thymine, cytosine) molecules. Weak hydrogen bonds formed between the probe molecule and the target DNA nucleobase enhance the electronic coupling and temporarily stabilize the translocating nucleobase against the orientational fluctuations, which may reduce noise in the current signal during experimental measurements. The findings of our density functional theory and non-equilibrium Green's function-based study indicate that this modeled setup could allow DNA nucleotide sequencing with a better and reliable yield, giving current traces that differ by at least 1 order of current magnitude for all the four target nucleotides. Thus, we feel that the functionalized armchair CNT (6,6) nanogap-embedded electrodes may be utilized for controlled DNA sequencing.
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Affiliation(s)
- Rameshwar L Kumawat
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
| | - Biswarup Pathak
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
- Discipline of Chemistry, School of Basic Sciences, Indian Institute of Technology (IIT) Indore Indore Madhya Pradesh 453552 India
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Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
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Hagan JT, Sheetz BS, Bandara YMNDY, Karawdeniya BI, Morris MA, Chevalier RB, Dwyer JR. Chemically tailoring nanopores for single-molecule sensing and glycomics. Anal Bioanal Chem 2020; 412:6639-6654. [PMID: 32488384 DOI: 10.1007/s00216-020-02717-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Brian S Sheetz
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Buddini I Karawdeniya
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Melissa A Morris
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Robert B Chevalier
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA.
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Pérez-Mitta G, Toimil-Molares ME, Trautmann C, Marmisollé WA, Azzaroni O. Molecular Design of Solid-State Nanopores: Fundamental Concepts and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1901483. [PMID: 31267585 DOI: 10.1002/adma.201901483] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Solid-state nanopores are fascinating objects that enable the development of specific and efficient chemical and biological sensors, as well as the investigation of the physicochemical principles ruling the behavior of biological channels. The great variety of biological nanopores that nature provides regulates not only the most critical processes in the human body, including neuronal communication and sensory perception, but also the most important bioenergetic process on earth: photosynthesis. This makes them an exhaustless source of inspiration toward the development of more efficient, selective, and sophisticated nanopore-based nanofluidic devices. The key point responsible for the vibrant and exciting advance of solid nanopore research in the last decade has been the simultaneous combination of advanced fabrication nanotechnologies to tailor the size, geometry, and application of novel and creative approaches to confer the nanopore surface specific functionalities and responsiveness. Here, the state of the art is described in the following critical areas: i) theory, ii) nanofabrication techniques, iii) (bio)chemical functionalization, iv) construction of nanofluidic actuators, v) nanopore (bio)sensors, and vi) commercial aspects. The plethora of potential applications once envisioned for solid-state nanochannels is progressively and quickly materializing into new technologies that hold promise to revolutionize the everyday life.
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Affiliation(s)
- Gonzalo Pérez-Mitta
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung, 64291, Darmstadt, Germany
- Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
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16
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Chen Q, Liu Z. Fabrication and Applications of Solid-State Nanopores. SENSORS 2019; 19:s19081886. [PMID: 31010038 PMCID: PMC6515193 DOI: 10.3390/s19081886] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 12/25/2022]
Abstract
Nanopores fabricated from synthetic materials (solid-state nanopores), platforms for characterizing biological molecules, have been widely studied among researchers. Compared with biological nanopores, solid-state nanopores are mechanically robust and durable with a tunable pore size and geometry. Solid-state nanopores with sizes as small as 1.3 nm have been fabricated in various films using engraving techniques, such as focused ion beam (FIB) and focused electron beam (FEB) drilling methods. With the demand of massively parallel sensing, many scalable fabrication strategies have been proposed. In this review, typical fabrication technologies for solid-state nanopores reported to date are summarized, with the advantages and limitations of each technology discussed in detail. Advanced shrinking strategies to prepare nanopores with desired shapes and sizes down to sub-1 nm are concluded. Finally, applications of solid-state nanopores in DNA sequencing, single molecule detection, ion-selective transport, and nanopatterning are outlined.
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Affiliation(s)
- Qi Chen
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
| | - Zewen Liu
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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18
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Le-The H, Tregouet C, Kappl M, Müller M, Kirchhoff K, Lohse D, van den Berg A, Odijk M, Eijkel JCT. Engulfment control of platinum nanoparticles into oxidized silicon substrates for fabrication of dense solid-state nanopore arrays. NANOTECHNOLOGY 2019; 30:065301. [PMID: 30523814 DOI: 10.1088/1361-6528/aaf114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We found that platinum (Pt) nanoparticles, upon annealing at high temperature of 1000 °C, are engulfed into amorphous fused-silica or thermal oxide silicon substrates. The same phenomenon was previously published for gold (Au) nanoparticles. Similar to the Au nanoparticles, the engulfed Pt nanoparticles connect to the surface of the substrates through conical nanopores, and the size of the Pt nanoparticles decreases with increasing depth of the nanopores. We explain the phenomena as driven by the formation of platinum oxide by reaction of the platinum with atmospheric oxygen, with platinum oxide evaporating to the environment. We found that the use of Pt provides much better controllability than the use of Au. Due to the high vapor pressure of platinum oxide, the engulfment of the Pt nanoparticles into oxidized silicon (SiO2) substrates is faster than of Au nanoparticles. At high temperature annealing we also find that the aggregation of Pt nanoparticles on the substrate surface is insignificant. As a result, the Pt nanoparticles are uniformly engulfed into the substrates, leading to an opportunity for patterning dense nanopore arrays. Moreover, the use of oxidized Si substrates enables us to precisely control the depth of the nanopores since the engulfment of Pt nanoparticles stops at a short distance above the SiO x /Si interface. After subsequent etching steps, a membrane with dense nanopore through-holes with diameters down to sub-30 nm is obtained. With its simple operation and high controllability, this fabrication method provides an alternative for rapid patterning of dense arrays of solid-state nanopores at low-cost.
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Affiliation(s)
- Hai Le-The
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, The Netherlands
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Bandara YMDY, Karawdeniya BI, Dwyer JR. Push-Button Method To Create Nanopores Using a Tesla-Coil Lighter. ACS OMEGA 2019; 4:226-230. [PMID: 31459326 PMCID: PMC6649298 DOI: 10.1021/acsomega.8b02660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/13/2018] [Indexed: 05/30/2023]
Abstract
Controlled dielectric breakdown (CDB) of silicon nitride thin films immersed in electrolyte solution has been used to fabricate single nanofluidic channels with ∼10 nm and smaller diameters, nanopores, useful in single-molecule sensing and ionic circuit construction. A hand-held Tesla-coil lighter was used to form nanofluidic ionic conductors through a ∼10 nm thick silicon nitride membrane. Modifications to the conventional approach were required by the low-overhead Tesla-coil-assisted method (TCAM): increased circuit resistance by including water in place of electrolyte and discrete rather than continuous voltage applications. The resulting ionic conductance could be tuned with the number of voltage applications. TCAM and conventional CDB produced nanopores with different conductance versus pH curves, suggesting different surface chemistry. Nevertheless, sensing experiments using the canonical test molecule, λ-DNA, produced signals comparable to translocation results through solid-state nanopores fabricated by other methods. Thus, the TCAM method offers flexibility in fabrication and in the properties and function of the nanoscale ionic conductors that it can generate.
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20
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Kumawat RL, Garg P, Kumar S, Pathak B. Electronic Transport through DNA Nucleotides in Atomically Thin Phosphorene Electrodes for Rapid DNA Sequencing. ACS APPLIED MATERIALS & INTERFACES 2019; 11:219-225. [PMID: 30540178 DOI: 10.1021/acsami.8b17239] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rapid progresses in developing the fast, low-cost, and reliable methods for DNA sequencing are envisaged for development of personalized medicine. In this respect, nanotechnology has paved the role for the development of advanced DNA sequencing techniques including sequencing with solid-state nanopores or nanogaps. Herein, we have explored the application of a black phosphorene based nanogap-device for DNA sequencing. Using density-functional-theory based non-equilibrium Green's function approach, we have computed transverse transmission and current-voltage ( I- V) characteristics of all the four DNA nucleotides (deoxy adenosine monophosphate, deoxy guanidine monophosphate, deoxy thymidine monophosphate, and deoxy cytosine monophosphate) as functions of applied bias voltages. We deduce that it is in principle; possible to differentiate between all the four nucleotides by three sequencing runs at distinct applied bias voltages, i.e., at 0.2, 1.4, and 1.6 V, where individual identification of all the four nucleotides may be possible. Hence, we believe our study might be helpful for experimentalist towards the development of a phosphorene based nanodevice for DNA sequencing to diagnose critical diseases.
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21
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He F, Liang L, Zhou S, Xie W, He S, Wang Y, Tlili C, Tong S, Wang D. Label-Free Sensitive Detection of Microcystin-LR via Aptamer-Conjugated Gold Nanoparticles Based on Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14825-14833. [PMID: 30021440 DOI: 10.1021/acs.langmuir.8b00945] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A versatile and highly sensitive strategy for nanopore detection of microcystin-LR (MC-LR) is proposed herein based on the aptamer and host-guest interactions by employing a gold nanoparticle (AuNP) probe. The aptamer of MC-LR and its complementary DNA (cDNA) are respectively immobilized on AuNPs with distinct sizes (5 nm AuNPs for the aptamer and 20 nm for the cDNA), and the constructed polymeric AuNP network via the hybridization of the aptamer and cDNA was disintegrated upon the addition of MC-LR. The specific interactions between the aptamer and MC-LR disrupt and release the cDNA-AuNPs that were then removed by centrifugation, leaving the MC-LR-aptamer-AuNP species in the supernatant for subsequent nanopore determination. By monitoring the current blockade of released MC-LR-aptamer-AuNPs using a specific tailored nanopore (10 and 20 nm in diameter, generated by current dielectric breakdown), we could deduce the presence of MC-LR, as the bulky NP network could not pass through a nanopore with a relatively smaller size. We realized the detection of MC-LR with a concentration as low as 0.1 nM; additionally, we have proved the specificity of the interaction between the aptamer and MC-LR by replacing MC-LR with other congener toxins (MC-RR and MC-YR), chlorophyll (a component abundantly coexists in water), and the mixture of the four.
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Affiliation(s)
- Feng He
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shuo Zhou
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Chaker Tlili
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shoufeng Tong
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
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22
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Zhang D, Zhou S, Liu Y, Fan X, Zhang M, Zhai J, Jiang L. Self-Assembled Porphyrin Nanofiber Membrane-Decorated Alumina Channels for Enhanced Photoelectric Response. ACS NANO 2018; 12:11169-11177. [PMID: 30376291 DOI: 10.1021/acsnano.8b05695] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Photoresponsive nanochannel systems whose ionic transportation properties can be controlled by the photoelectric effect, such as for green chlorophyll pigments in plants, are attracting widespread attention. Herein, we prepared photoresponsive heterogeneous nanochannels by decorating self-assembled tetra(4-sulfonatophenyl)porphyrin (TPPS) nanofiber membranes on a membrane of hourglass-shaped alumina (Al2O3) nanochannels using the diffusion-limited patterning (DLP) method. The close arrangement of large-area nanofibers promoted the photoresponse sensitivity of the heterogeneous nanochannels, which showed the highest ionic transportation current. With illumination comparable to sunlight in intensity, the photoresponsive ionic current was approximately 9.7 μA, demonstrating photoswitching, which could be used to regulate the reversible transformation of ionic currents. Meanwhile, the cooperative effect of the TPPS nanofibers assembled at the entrance to the nanochannels and the TPPS molecules inside the nanochannels allowed the heterogeneous nanochannels to exhibit a good rectifying performance.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Shuqi Zhou
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - You Liu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Xia Fan
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Mingliang Zhang
- Engineering Research Center for Semiconductor Integrated Technology, Institute of Semiconductors , Chinese Academy of Sciences , Beijing 100083 , People's Republic of China
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Beijing 101408 , People's Republic of China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
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Zhang D, Wang Q, Fan X, Zhang M, Zhai J, Jiang L. An Effective Dark-Vis-UV Ternary Biomimetic Switching Based on N3/Spiropyran-Modified Nanochannels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1804862. [PMID: 30284330 DOI: 10.1002/adma.201804862] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Many natural photomodulated nanochannels are investigated and are crucial for biological activity. Biomimetic nanochannels with a bistable conductance state under light stimulus are demonstrated. In this system, two molecules, cis-bis-(4,4'-dicarboxy-2,2'-bipyridine) dithiocyanato ruthenium(II) (N3) and spiropyran 1'-(3-carboxypropyl)-3',3'-dimethyl-6-nitro-spiro[2H-1]benzopyran-2,2'-indoline (SP-COOH), each with unique photoresponsive properties, are modified in alumina nanochannels. The two segments of the hourglass-shaped alumina nanochannels are designated to graft a certain molecule. Under ultraviolet (UV) or visible light (vis) irradiation, electrons belonging to N3 are excited, resulting in negatively charged surfaces on the sides of nanochannels modified with N3 molecules. Only under UV stimulus, the conformation change of the SP-COOH molecules leads to positively charged surfaces of nanochannels in the SP-COOH occupied sides. Benefiting from the joint effect of N3 and SP-COOH, low, medium, and high (i.e., "0," "1," and "2") ternary levels of ion conductance are established under the dark-vis-UV alternate stimuli. The multistage current switching containing "0-1-2-0" and "0-1-2-1-0" procedures is stable and robust. Additionally, the diode-like ion transport behavior of the nanochannels could be exploited to support a multivalued logical gating with the management of light signals.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Qinqin Wang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Xia Fan
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Mingliang Zhang
- Engineering Research Center for Semiconductor Integrated Technology, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 101408, P. R. China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
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Abstract
Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.
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25
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Burden DL, Kim D, Cheng W, Chandler Lawler E, Dreyer DR, Keranen Burden LM. Mechanically Enhancing Planar Lipid Bilayers with a Minimal Actin Cortex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10847-10855. [PMID: 30149716 DOI: 10.1021/acs.langmuir.8b01847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
All cells in all domains of life possess a cytoskeleton that provides mechanical resistance to deformation and general stability to the plasma membrane. Here, we utilize a two-dimensional scaffolding created by actin filaments to convey mechanical support upon relatively fragile planar bilayer membranes (black lipid membranes, BLMs). Robust biomembranes play a critical role in the development of protein nanopore sensor applications and might also prove helpful in ion-channel research. Our investigation utilizes a minimal actin cortex (MAC) that is formed by anchoring actin filaments to lipid membranes via a biotin-streptavidin-biotin bridge. We characterize the joined structure using various modes of optical microscopy, electrophysiology, and applied mechanical stress (including measurements of elastic modulus). Our findings show the resulting structure includes a thin supporting layer of actin. Electrical studies indicate that the integrity of the MAC-bilayer composite remains unchanged over the limits of our tests (i.e., hours to days). The actin filament structure can remain intact for months. Minimalistic layering of the actin support network produces an increase in the apparent elastic modulus of the MAC-derivatized bilayer by >100×, compared to unmodified BLMs. Furthermore, the resistance to applied stress improves with the number of actin layers, which can be cross-linked to arbitrary thicknesses, in principle. The weblike support structure retains the lateral fluidity of the BLM, maintains the high electrical resistance typical of traditional BLMs, enables relatively uninhibited molecular access to the lipid surface from bulk solution, and permits nanopore self-assembly and insertion in the bilayer. These interfacial features are highly desirable for ion-channel and nanopore sensing applications.
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Affiliation(s)
- Daniel L Burden
- Chemistry Department , Wheaton College , Wheaton , Illinois 60187 , United States
| | - Daniel Kim
- Chemistry Department , Wheaton College , Wheaton , Illinois 60187 , United States
| | - Wayland Cheng
- Chemistry Department , Wheaton College , Wheaton , Illinois 60187 , United States
| | | | - Daniel R Dreyer
- Chemistry Department , Wheaton College , Wheaton , Illinois 60187 , United States
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Xu Y. Nanofluidics: A New Arena for Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1702419. [PMID: 29094401 DOI: 10.1002/adma.201702419] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/04/2017] [Indexed: 06/07/2023]
Abstract
A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.
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Affiliation(s)
- Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
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Wang S, Zhao Z, Haque F, Guo P. Engineering of protein nanopores for sequencing, chemical or protein sensing and disease diagnosis. Curr Opin Biotechnol 2017; 51:80-89. [PMID: 29232619 DOI: 10.1016/j.copbio.2017.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/17/2022]
Abstract
Biological systems contain highly-ordered structures performing diverse functions. The elegant structures of biomachines have inspired the development of nanopores as single molecule sensors. Over the years, the utility of nanopores for detecting a wide variety of analytes have rapidly emerged for sensing, sequencing and diagnostic applications. Several protein channels with diverse shapes and sizes, such as motor channels from bacteriophage Phi29, SPP1, T3, and T4, as well as α-hemolysin, MspA, aerolysin, FluA, OmpF/G, CsgG, ClyA, have been continually investigated and developed as nanopores. Herein, we focus on advances in biological nanopores for single molecule sensing and DNA sequencing from a protein engineering standpoint for changing pore sizes, altering charge distributions, enhancing sensitivity, improving stability, and imparting new detection capabilities.
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Affiliation(s)
| | - Zhengyi Zhao
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | | | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics & Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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28
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Bandara YMNDY, Nichols JW, Iroshika Karawdeniya B, Dwyer JR. Conductance‐based profiling of nanopores: Accommodating fabrication irregularities. Electrophoresis 2017; 39:626-634. [DOI: 10.1002/elps.201700299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Jason R. Dwyer
- Department of Chemistry University of Rhode Island Kingston RI USA
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29
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Jain T, Rasera BC, Guerrero RJS, Lim JM, Karnik R. Microfluidic multiplexing of solid-state nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:484001. [PMID: 29116942 DOI: 10.1088/1361-648x/aa9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although solid-state nanopores enable electronic analysis of many clinically and biologically relevant molecular structures, there are few existing device architectures that enable high-throughput measurement of solid-state nanopores. Herein, we report a method for microfluidic integration of multiple solid-state nanopores at a high density of one nanopore per (35 µm2). By configuring microfluidic devices with microfluidic valves, the nanopores can be rinsed from a single fluid input while retaining compatibility for multichannel electrical measurements. The microfluidic valves serve the dual purpose of fluidic switching and electric switching, enabling serial multiplexing of the eight nanopores with a single pair of electrodes. Furthermore, the device architecture exhibits low noise and is compatible with electroporation-based in situ nanopore fabrication, providing a scalable platform for automated electronic measurement of a large number of integrated solid-state nanopores.
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Affiliation(s)
- Tarun Jain
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, United States of America
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30
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Yin B, Xie W, Liang L, Deng Y, He S, He F, Zhou D, Tlili C, Wang D. Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection. ACS OMEGA 2017; 2:7127-7135. [PMID: 31457292 PMCID: PMC6645049 DOI: 10.1021/acsomega.7b01245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/06/2017] [Indexed: 05/11/2023]
Abstract
In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.
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31
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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32
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Song Y, Zhang J, Li D. Microfluidic and Nanofluidic Resistive Pulse Sensing: A Review. MICROMACHINES 2017; 8:E204. [PMID: 30400393 PMCID: PMC6190343 DOI: 10.3390/mi8070204] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/11/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
Abstract
The resistive pulse sensing (RPS) method based on the Coulter principle is a powerful method for particle counting and sizing in electrolyte solutions. With the advancement of micro- and nano-fabrication technologies, microfluidic and nanofluidic resistive pulse sensing technologies and devices have been developed. Due to the unique advantages of microfluidics and nanofluidics, RPS sensors are enabled with more functions with greatly improved sensitivity and throughput and thus have wide applications in fields of biomedical research, clinical diagnosis, and so on. Firstly, this paper reviews some basic theories of particle sizing and counting. Emphasis is then given to the latest development of microfuidic and nanofluidic RPS technologies within the last 6 years, ranging from some new phenomena, methods of improving the sensitivity and throughput, and their applications, to some popular nanopore or nanochannel fabrication techniques. The future research directions and challenges on microfluidic and nanofluidic RPS are also outlined.
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Affiliation(s)
- Yongxin Song
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Junyan Zhang
- Department of Marine Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Dongqing Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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33
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Bandara YMNDY, Karawdeniya BI, Whelan JC, Ginsberg LDS, Dwyer JR. Solution-Based Photo-Patterned Gold Film Formation on Silicon Nitride. ACS APPLIED MATERIALS & INTERFACES 2016; 8:34964-34969. [PMID: 27936582 DOI: 10.1021/acsami.6b12720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silicon nitride fabricated by low-pressure chemical vapor deposition (LPCVD) to be silicon-rich (SiNx), is a ubiquitous insulating thin film in the microelectronics industry, and an exceptional structural material for nanofabrication. Free-standing <100 nm thick SiNx membranes are especially compelling, particularly when used to deliver forefront molecular sensing capabilities in nanofluidic devices. We developed an accessible, gentle, and solution-based photodirected surface metallization approach well-suited to forming patterned metal films as integral structural and functional features in thin-membrane-based SiNx devices-for use as electrodes or surface chemical functionalization platforms, for example-augmenting existing device capabilities and properties for a wide range of applications.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Buddini Iroshika Karawdeniya
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Julie C Whelan
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Lucas D S Ginsberg
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
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Dwyer JR, Bandara YMNDY, Whelan JC, Karawdeniya BI, Nichols JW. Silicon Nitride Thin Films for Nanofluidic Device Fabrication. NANOFLUIDICS 2016. [DOI: 10.1039/9781849735230-00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
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Affiliation(s)
- J. R. Dwyer
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | | | - J. C. Whelan
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - B. I. Karawdeniya
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - J. W. Nichols
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
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35
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Bandara YMNDY, Karawdeniya BI, Dwyer JR. Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication. ACS APPLIED MATERIALS & INTERFACES 2016; 8:30583-30589. [PMID: 27709879 DOI: 10.1021/acsami.6b10045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a method for simply characterizing the size and shape of a nanopore during solution-based fabrication and surface modification, using only low-overhead approaches native to conventional nanopore measurements. Solution-based nanopore fabrication methods are democratizing nanopore science by supplanting the traditional use of charged-particle microscopes for fabrication, but nanopore profiling has customarily depended on microscopic examination. Our approach exploits the dependence of nanopore conductance in solution on nanopore size, shape, and surface chemistry in order to characterize nanopores. Measurements of the changing nanopore conductance during formation by etching or deposition can be analyzed using our method to characterize the nascent nanopore size and shape, beyond the typical cylindrical approximation, in real-time. Our approach thus accords with ongoing efforts to broaden the accessibility of nanopore science from fabrication through use: it is compatible with conventional instrumentation and offers straightforward nanoscale characterization of the core tool of the field.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Buddini Iroshika Karawdeniya
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
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36
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Abstract
Nanoscale fluid transport through conduits in the 1-100 nm range is termed as nanofluidics. Over the past decade or so, significant scientific and technological advances have occurred in the domain of nanofluidics with a transverse external electrical signal through a dielectric layer permitting control over ionic and fluid flows in these nanoscale conduits. Consequently, this special class of nanofluidic devices is commonly referred to as field effect devices, analogous to the solid-state field effect transistors that form the basis for modern electronics. In this mini-review, we focus on summarizing the recent developments in field effect nanofluidics as a discipline and evaluate both tutorially and critically the scientific and technological advances that have been reported, including a discussion on the future outlook and identifying broad open questions which suggest that there are many breakthroughs still to come in field-effect nanofluidics.
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Affiliation(s)
- Shaurya Prakash
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - A T Conlisk
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
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37
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Rems L, Kawale D, Lee LJ, Boukany PE. Flow of DNA in micro/nanofluidics: From fundamentals to applications. BIOMICROFLUIDICS 2016; 10:043403. [PMID: 27493701 PMCID: PMC4958106 DOI: 10.1063/1.4958719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023]
Abstract
Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.
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Affiliation(s)
- Lea Rems
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - Durgesh Kawale
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - L James Lee
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, Ohio 43210, USA
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
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38
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Hsiao PY. Polyelectrolyte Threading through a Nanopore. Polymers (Basel) 2016; 8:E73. [PMID: 30979169 PMCID: PMC6432567 DOI: 10.3390/polym8030073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/02/2023] Open
Abstract
Threading charged polymers through a nanopore, driven by electric fields E, is investigated by means of Langevin dynamics simulations. The mean translocation time 〈 τ 〉 is shown to follow a scaling law Nα, and the exponent α increases monotonically from 1.16 (4) to 1.40 (3) with E. The result is double-checked by the calculation of mean square displacement of translocation coordinate, which asserts a scaling behavior tβ (for t near τ) with β complying with the relation αβ = 2. At a fixed chain length N, 〈τ〉 displayed a reciprocal scaling behavior E-1 in the weak and also in the strong fields, connected by a transition E-1.64(5) in the intermediate fields. The variations of the radius of gyration of chain and the positions of chain end are monitored during a translocation process; far-from-equilibrium behaviors are observed when the driving field is strong. A strong field can strip off the condensed ions on the chain when it passes the pore. The total charges of condensed ions are hence decreased. The studies for the probability and density distributions reveal that the monomers in the trans-region are gathered near the wall and form a pancake-like density profile with a hump cloud over it in the strong fields, due to fast translocation.
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Affiliation(s)
- Pai-Yi Hsiao
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
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39
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Ding Y, Kanavarioti A. Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:91-101. [PMID: 26925357 PMCID: PMC4734350 DOI: 10.3762/bjnano.7.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
The influence of an electric field on an isolated channel or nanopore separating two compartments filled with electrolytes produces a constant ion flux through the pore. Nucleic acids added to one compartment traverse the pore, and modulate the current in a sequence-dependent manner. While translocation is faster than detection, the α-hemolysin nanopore (α-HL) successfully senses base modifications in ssDNA immobilized within the pore. With the assistance of a processing enzyme to slow down translocation, nanopore-based DNA sequencing is now a commercially available platform. However, accurate base calling is challenging because α-HL senses a sequence, and not a single nucleotide. Osmylated DNA was recently proposed as a surrogate for nanopore-based sequencing. Osmylation is the addition of osmium tetroxide 2,2'-bipyridine (OsBp) to the C5-C6 pyrimidine double bond. The process is simple, selective for deoxythymidine (dT) over deoxycytidine (dC), unreactive towards the purines, practically 100% effective, and strikingly independent of length, sequence, and composition. Translocation of an oligodeoxynucleotide (oligo) dA10XdA9 via α-HL is relatively slow, and exhibits distinct duration as well as distinct residual current when X = dA, dT(OsBp), or dC(OsBp). The data indicate that the α-HL constriction zone/β-barrel interacts strongly with both OsBp and the base. A 23 nucleotide long oligo with four dT(OsBp) traverses 18-times slower, and the same oligo with nine (dT+dC)(OsBp) moieties traverses 84-times slower compared to dA20, suggesting an average rate of 40 or 180 μs/base, respectively. These translocation speeds are well above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA.
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Affiliation(s)
- Yun Ding
- Chemistry Department, University of Utah, Salt Lake City, UT, USA
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40
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Varricchio SSG, Cyrille H, Arnaud B, Philippe R. Fabrication of multilayered nanofluidic membranes through silicon templates. NANOSCALE 2015; 7:20451-9. [PMID: 26584307 DOI: 10.1039/c5nr05288b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present a new fabrication method for solid-state nanoporous membranes based on sacrificial template structures made of silicon. The process consists of creating membranes by evaporating thin-films on sacrificial templates which, after their selective removal, opens the nanopores and releases the free-standing membranes. This way it is possible to define the geometry of the pore by design and to build the membrane by stacking thin-films of various materials through evaporation. Such a membrane with controlled porosity, pore geometry, thickness and nano-channel composition provides new opportunities for selective chemical functionalization, gating, electrical sensing or electrical stimulation inside the nanopore.
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Affiliation(s)
| | - Hibert Cyrille
- Center of MicroNanoTechnology, EPFL, CH-1015 Lausanne, Switzerland
| | - Bertsch Arnaud
- EPFL STI IMT LMIS4, Station 17, CH-1015 Lausanne, Switzerland.
| | - Renaud Philippe
- EPFL STI IMT LMIS4, Station 17, CH-1015 Lausanne, Switzerland.
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