1
|
Ivanov YD, Ableev AN, Vinogradova AV, Nevedrova ED, Shumov ID, Ziborov VS, Kozlov AF, Ivanova IA, Vaulin NV, Lebedev DV, Bukatin AS, Mukhin IS, Ponomarenko EA, Archakov AI. Registration of activity of a single molecule of horseradish peroxidase using a detector based on a solid-state nanopore. BIOMEDITSINSKAIA KHIMIIA 2024; 70:349-355. [PMID: 39324199 DOI: 10.18097/pbmc20247005349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
This work demonstrates the use of a solid-state nanopore detector to monitor the activity of a single molecule of a model enzyme, horseradish peroxidase (HRP). This detector includes a measuring cell, which is divided into cis- and trans- chambers by a silicon nitride chip (SiN structure) with a nanopore of 5 nm in diameter. To entrap a single HRP molecule into the nanopore, an electrode had been placed into the cis-chamber; HRP solution was added into this chamber after application of a negative voltage. The reaction of the HRP substrate, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), oxidation by the enzyme molecule was performed in the presence of hydrogen peroxide. During this reaction, the functioning of a single HRP molecule, entrapped in the nanopore, was monitored by recording the time dependence of the ion current flowing through the nanopore. The approach proposed in our work is applicable for further studies of functioning of various enzymes at the level of single molecules, and this is an important step in the development of single-molecule enzymology.
Collapse
Affiliation(s)
- Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A N Ableev
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - I D Shumov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V S Ziborov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A F Kozlov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - I A Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - N V Vaulin
- Alferov University, St. Petersburg, Russia; Institute for Analytical Instrumentation, St. Petersburg, Russia
| | - D V Lebedev
- Alferov University, St. Petersburg, Russia; Institute for Analytical Instrumentation, St. Petersburg, Russia
| | - A S Bukatin
- Alferov University, St. Petersburg, Russia; Institute for Analytical Instrumentation, St. Petersburg, Russia
| | - I S Mukhin
- Alferov University, St. Petersburg, Russia; Institute for Analytical Instrumentation, St. Petersburg, Russia
| | | | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
2
|
Tao C, Bai Y, Chen J, Lu J, Bi Y, Li J. Detection of Glutamate Decarboxylase Antibodies and Simultaneous Multi-Molecular Translocation Exploration by Glass Nanopores. BIOSENSORS 2024; 14:255. [PMID: 38785729 PMCID: PMC11118187 DOI: 10.3390/bios14050255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Glutamic acid decarboxylase antibody (GADAb) has emerged as a significant biomarker for clinical diagnosis and prognosis in type 1 diabetes (T1D). In this study, we investigated the potential utilization of glass capillary solid-state nanopores as a cost-effective and easily preparable platform for the detection of individual antigens, antibodies, and antigen-antibody complexes without necessitating any modifications to the nanopores. Our findings revealed notable characteristic variations in the translocation events of glutamic acid decarboxylase (GAD65) through nanopores under different voltage conditions, discovered that anomalous phenomenon of protein translocation events increasing with voltage may potentially be caused by the crowding of multiple proteins in the nanopores, and demonstrated that there are multiple components in the polyclonal antibodies (GADAb-poly). Furthermore, we achieved successful differentiation between GAD65, GADAb, and GADAb-GAD65 complexes. These results offer promising prospects for the development of a rapid and reliable GADAb detection method, which holds the potential to be applied in patient serum samples, thereby facilitating a label-free, cost-effective, and early diagnosis of type I diabetes.
Collapse
Affiliation(s)
- Chongxin Tao
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Jing Lu
- Department of Endocrinology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yan Bi
- Department of Endocrinology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| |
Collapse
|
3
|
Jodeyri Z, Taghipoor M. Multivariate analysis of nanoparticle translocation through a nanopore to improve the accuracy of resistive pulse sensing. Phys Chem Chem Phys 2024; 26:5097-5105. [PMID: 38259043 DOI: 10.1039/d3cp05565e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The advent of nanopore-based sensors based on resistive pulse sensing gave rise to a remarkable breakthrough in the detection and characterization of nanoscale species. Some strong correlations have been reported between the resistive pulse characteristics and the particle's geometrical and physical properties. These correlations are commonly used to obtain information about the particles in commercial devices and research setups. The correlations, however, do not consider the simultaneous effect of influential factors such as particle shape and off-axis translocation, which complicates the extraction of accurate information from the resistive pulses. In this paper, we numerically studied the impact of the shape and position of particles on pulse characteristics in order to estimate the errors that arise from neglecting the influence of multiple factors on resistive pulses. We considered the sphere, oblate, and prolate particles to investigate the nanoparticle shape effect. Moreover, the trajectory dependency was examined by considering the translocation of nanoparticles away from the nanopore axis. Meanwhile, the shape effect was studied for different trajectories. We observed that the simultaneous effects of influential parameters could lead to significant errors in estimating particle properties if the coupled effects are neglected. Based on the results, we introduce the "pulse waveshape" as a novel characteristic of the resistive pulse that can be utilized as a decoupling parameter in the analysis of resistive pulses.
Collapse
Affiliation(s)
- Zohre Jodeyri
- Micro Nano Systems Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| | - Mojtaba Taghipoor
- Micro Nano Systems Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
| |
Collapse
|
4
|
Guan X, Shao W, Zhang D. T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition. Bioinformatics 2024; 40:btae083. [PMID: 38366607 PMCID: PMC10902682 DOI: 10.1093/bioinformatics/btae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
MOTIVATION Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy. RESULTS Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length. AVAILABILITY AND IMPLEMENTATION The main program is available at https://github.com/guanxiaoyu11/S2Inet.
Collapse
Affiliation(s)
- Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
- Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Wei Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
- Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
- Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| |
Collapse
|
5
|
Zhang HF, Delaidelli A, Javed S, Turgu B, Morrison T, Hughes CS, Yang X, Pachva M, Lizardo MM, Singh G, Hoffmann J, Huang YZ, Patel K, Shraim R, Kung SH, Morin GB, Aparicio S, Martinez D, Maris JM, Bosse KR, Williams KC, Sorensen PH. A MYCN-independent mechanism mediating secretome reprogramming and metastasis in MYCN-amplified neuroblastoma. SCIENCE ADVANCES 2023; 9:eadg6693. [PMID: 37611092 PMCID: PMC10446492 DOI: 10.1126/sciadv.adg6693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
MYCN amplification (MNA) is a defining feature of high-risk neuroblastoma (NB) and predicts poor prognosis. However, whether genes within or in close proximity to the MYCN amplicon also contribute to MNA+ NB remains poorly understood. Here, we identify that GREB1, a transcription factor encoding gene neighboring the MYCN locus, is frequently coexpressed with MYCN and promotes cell survival in MNA+ NB. GREB1 controls gene expression independently of MYCN, among which we uncover myosin 1B (MYO1B) as being highly expressed in MNA+ NB and, using a chick chorioallantoic membrane (CAM) model, as a crucial regulator of invasion and metastasis. Global secretome and proteome profiling further delineates MYO1B in regulating secretome reprogramming in MNA+ NB cells, and the cytokine MIF as an important pro-invasive and pro-metastatic mediator of MYO1B activity. Together, we have identified a putative GREB1-MYO1B-MIF axis as an unconventional mechanism promoting aggressive behavior in MNA+ NB and independently of MYCN.
Collapse
Affiliation(s)
- Hai-Feng Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Sumreen Javed
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Busra Turgu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Taylor Morrison
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christopher S. Hughes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Xiaqiu Yang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Manideep Pachva
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael M. Lizardo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gurdeep Singh
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Jennifer Hoffmann
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yue Zhou Huang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Khushbu Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Daniel Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla C. Williams
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Poul H. Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| |
Collapse
|
6
|
Dong J, Qiu X, Huang M, Chen X, Li Y. G-quadruplex-hemin DNAzyme functionalized nanopipettes: Fabrication and sensing application. Talanta 2023; 257:124384. [PMID: 36812658 DOI: 10.1016/j.talanta.2023.124384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
Solid-nanopores/nanopipettes have the exquisite ability to reveal the changes in molecular volume due to the advantages of adjustable size, good rigidity and low noise. Herein, a new platform for sensing application was established based on G-quadruplex-hemin DNAzyme (GQH) functionalized gold-coated nanopipettes. In this method, GQH was immobilized on gold-coated nanopipette, which could be used as a catalyst for the reaction of H2O2 with 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) to promote the conversion of ABTS to ABTS+ ions inside gold-coated nanopipette, and the change of transmembrane ion current could be monitored in real time. At the optimal conditions, there was a correlation between the ion current and the concentration of H2O2 in a certain range, which could be used for the hydrogen peroxide sensing. The GQH immobilized nanopipette provides a useful platform to investigate enzymatic catalysis in confined environment, which can be used in electrocatalysis, sensing and fundamental electrochemistry.
Collapse
Affiliation(s)
- Jingyi Dong
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Mimi Huang
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xiaohu Chen
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China.
| |
Collapse
|
7
|
Wang X, Thomas TM, Ren R, Zhou Y, Zhang P, Li J, Cai S, Liu K, Ivanov AP, Herrmann A, Edel JB. Nanopore Detection Using Supercharged Polypeptide Molecular Carriers. J Am Chem Soc 2023; 145:6371-6382. [PMID: 36897933 PMCID: PMC10037339 DOI: 10.1021/jacs.2c13465] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The analysis at the single-molecule level of proteins and their interactions can provide critical information for understanding biological processes and diseases, particularly for proteins present in biological samples with low copy numbers. Nanopore sensing is an analytical technique that allows label-free detection of single proteins in solution and is ideally suited to applications, such as studying protein-protein interactions, biomarker screening, drug discovery, and even protein sequencing. However, given the current spatiotemporal limitations in protein nanopore sensing, challenges remain in controlling protein translocation through a nanopore and relating protein structures and functions with nanopore readouts. Here, we demonstrate that supercharged unstructured polypeptides (SUPs) can be genetically fused with proteins of interest and used as molecular carriers to facilitate nanopore detection of proteins. We show that cationic SUPs can substantially slow down the translocation of target proteins due to their electrostatic interactions with the nanopore surface. This approach enables the differentiation of individual proteins with different sizes and shapes via characteristic subpeaks in the nanopore current, thus facilitating a viable route to use polypeptide molecular carriers to control molecular transport and as a potential system to study protein-protein interactions at the single-molecule level.
Collapse
Affiliation(s)
- Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Tina-Marie Thomas
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, U.K
| | - Yu Zhou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Peng Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| |
Collapse
|
8
|
Guan X, Li H, Chen L, Qi G, Jin Y. Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection. ACS Sens 2023; 8:427-442. [PMID: 36670058 DOI: 10.1021/acssensors.2c02102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.
Collapse
Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| |
Collapse
|
9
|
Liu H, Zhou Q, Wang W, Fang F, Zhang J. Solid-State Nanopore Array: Manufacturing and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205680. [PMID: 36470663 DOI: 10.1002/smll.202205680] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Nanopore brings extraordinary properties for a variety of potential applications in various industrial sectors. Since manufacturing of solid-state nanopore is first reported in 2001, solid-state nanopore has become a hot topic in the recent years. An increasing number of manufacturing methods have been reported, with continuously decreased sizes from hundreds of nanometers at the beginning to ≈1 nm until recently. To enable more robust, sensitive, and reliable devices required by the industry, researchers have started to explore the possible methods to manufacture nanopore array which presents unprecedented challenges on the fabrication efficiency, accuracy and repeatability, applicable materials, and cost. As a result, the exploration of fabrication of nanopore array is still in the fledging period with various bottlenecks. In this article, a wide range of methods of manufacturing nanopores are summarized along with their achievable morphologies, sizes, inner structures for characterizing the main features, based on which the manufacturing of nanopore array is further addressed. To give a more specific idea on the potential applications of nanopore array, some representative practices are introduced such as DNA/RNA sequencing, energy conversion and storage, water desalination, nanosensors, nanoreactors, and dialysis.
Collapse
Affiliation(s)
- Hongshuai Liu
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Qin Zhou
- College of Basic Medicine, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang, 150081, China
| | - Wei Wang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, 2006 Xiyuan Ave, Chengdu, Sichuan, 611731, China
| | - Fengzhou Fang
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
- State Key Laboratory of Precision Measuring Technology and Instruments, Laboratory of Micro/Nano Manufacturing Technology (MNMT), Tianjin University, Tianjin, 300072, China
| | - Jufan Zhang
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
| |
Collapse
|
10
|
Cao M, Zhang L, Tang H, Qiu X, Li Y. Single-Molecule Investigation of the Protein-Aptamer Interactions and Sensing Application Inside the Single Glass Nanopore. Anal Chem 2022; 94:17405-17412. [PMID: 36475604 DOI: 10.1021/acs.analchem.2c02660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solid-state nanopores offer a nanoconfined space for a single-molecule sensing strategy. Evaluating the behavior of proteins and protein-related interactions at the single-molecule level is becoming more and more important for a better understanding of biological processes and diseases. In this work, the aptamer-functionalized nanopore was prepared as the sensing platform for kinetic analysis of the carcinoembryonic antigen (CEA) with its aptamers, which is an important cancer biomarker. CEA molecules were captured by the aptamers immobilized on the inner surface of the nanopore, and there was a complicated interaction between the CEA molecules and the aptamer, which is the process of association and dissociation. This could be used to measure the dynamics of aptamer-protein interactions without labeling. The kinetic analysis could be evaluated at the single-molecule level to interpret the dissociation constants of the binding and dissociation processes. Results showed that the translocation of CEA molecules in a functionalized nanopore had a deep blockades degree and long duration compared with nanopore modified with bare gold, which could be used for CEA sensing. This protein and protein-related interaction we designed provides new insights for evaluating the binding affinity, which will be beneficial for protein sensing and immunoassays.
Collapse
Affiliation(s)
- Mengya Cao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Lijun Zhang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Xia Qiu
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| |
Collapse
|
11
|
Guan X, Li Z, Zhou Y, Shao W, Zhang D. Active learning for efficient analysis of high-throughput nanopore data. Bioinformatics 2022; 39:6851141. [PMID: 36445037 PMCID: PMC9825740 DOI: 10.1093/bioinformatics/btac764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/25/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION As the third-generation sequencing technology, nanopore sequencing has been used for high-throughput sequencing of DNA, RNA, and even proteins. Recently, many studies have begun to use machine learning technology to analyze the enormous data generated by nanopores. Unfortunately, the success of this technology is due to the extensive labeled data, which often suffer from enormous labor costs. Therefore, there is an urgent need for a novel technology that can not only rapidly analyze nanopore data with high-throughput, but also significantly reduce the cost of labeling. To achieve the above goals, we introduce active learning to alleviate the enormous labor costs by selecting the samples that need to be labeled. This work applies several advanced active learning technologies to the nanopore data, including the RNA classification dataset (RNA-CD) and the Oxford Nanopore Technologies barcode dataset (ONT-BD). Due to the complexity of the nanopore data (with noise sequence), the bias constraint is introduced to improve the sample selection strategy in active learning. Results: The experimental results show that for the same performance metric, 50% labeling amount can achieve the best baseline performance for ONT-BD, while only 15% labeling amount can achieve the best baseline performance for RNA-CD. Crucially, the experiments show that active learning technology can assist experts in labeling samples, and significantly reduce the labeling cost. Active learning can greatly reduce the dilemma of difficult labeling of high-capacity nanopore data. We hope active learning can be applied to other problems in nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION The main program is available at https://github.com/guanxiaoyu11/AL-for-nanopore. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
| | - Zhongnian Li
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China,School of Computer Science, China University of Mining Technology, Xuzhou 221116, China
| | - Yueying Zhou
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
| | - Wei Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
| | | |
Collapse
|
12
|
Ma J, Wang S, Wan X, Ma D, Xiao Y, Hao Q, Yang N. The unrevealed 3D morphological evolution of annealed nanoporous thin films. NANOSCALE 2022; 14:17072-17079. [PMID: 36373437 DOI: 10.1039/d2nr04014j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanoporous materials (sub-10 nm in diameter) have potential applications in chips, biosensors, thermoelectrics, desalination and other fields due to their large surface-to-volume ratio. Thermal annealing is a preferred technique to precisely control the ultra-fine nanopore size. Here, the 3D morphological evolution of a membrane with periodic nanopores by thermal annealing is studied. It is found that the evolution is determined by the combination of the membrane thickness, the initial nanopore radius and the periodic length of the porous pattern, rather than the previously suggested ratio between the membrane thickness and pore radius. High-temperature annealing experiments and molecular dynamics simulations are performed to confirm the rationality of the newly proposed model. Energy analysis demonstrates that surface energy minimization is the driving force of the morphological evolution. The local minimum of energy in the new model provides the possibility of thermal stability of nanoporous silicon as a thermoelectric material. This study provides guidance for the mass production of nanoporous membranes with high-temperature annealing.
Collapse
Affiliation(s)
- Jianqiang Ma
- School of Energy and Power Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Sien Wang
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721-0119, USA.
| | - Xiao Wan
- School of Energy and Power Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Dengke Ma
- NNU-SULI Thermal Energy Research Center (NSTER) & Center for Quantum Transport and Thermal Energy Science (CQTES), School of Physics and Technology, Nanjing Normal University, Nanjing 210023, China
| | - Yue Xiao
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721-0119, USA.
| | - Qing Hao
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721-0119, USA.
| | - Nuo Yang
- School of Energy and Power Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| |
Collapse
|
13
|
Dynamic rotation featured translocations of human serum albumin with a conical glass nanopore. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
14
|
Lastra LS, Bandara YMNDY, Nguyen M, Farajpour N, Freedman KJ. On the origins of conductive pulse sensing inside a nanopore. Nat Commun 2022; 13:2186. [PMID: 35562332 PMCID: PMC9106702 DOI: 10.1038/s41467-022-29758-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Nanopore sensing is nearly synonymous with resistive pulse sensing due to the characteristic occlusion of ions during pore occupancy, particularly at high salt concentrations. Contrarily, conductive pulses are observed under low salt conditions wherein electroosmotic flow is significant. Most literature reports counterions as the dominant mechanism of conductive events (a molecule-centric theory). However, the counterion theory does not fit well with conductive events occurring via net neutral-charged protein translocation, prompting further investigation into translocation mechanics. Herein, we demonstrate theory and experiments underpinning the translocation mechanism (i.e., electroosmosis or electrophoresis), pulse direction (i.e., conductive or resistive) and shape (e.g., monophasic or biphasic) through fine control of chemical, physical, and electronic parameters. Results from these studies predict strong electroosmosis plays a role in driving DNA events and generating conductive events due to polarization effects (i.e., a pore-centric theory). Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.
Collapse
Affiliation(s)
- Lauren S Lastra
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Michelle Nguyen
- Department of Biology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| |
Collapse
|
15
|
Choudhary A, Maffeo C, Aksimentiev A. Multi-resolution simulation of DNA transport through large synthetic nanostructures. Phys Chem Chem Phys 2022; 24:2706-2716. [PMID: 35050282 PMCID: PMC8855663 DOI: 10.1039/d1cp04589j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method - the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore - is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities.
Collapse
Affiliation(s)
- Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
16
|
Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
Collapse
|
17
|
Akhtarian S, Miri S, Doostmohammadi A, Brar SK, Rezai P. Nanopore sensors for viral particle quantification: current progress and future prospects. Bioengineered 2021; 12:9189-9215. [PMID: 34709987 PMCID: PMC8810133 DOI: 10.1080/21655979.2021.1995991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.
Collapse
Affiliation(s)
- Shiva Akhtarian
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Saba Miri
- Department of Civil Engineering, York University, Toronto, ON, Canada
| | - Ali Doostmohammadi
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| |
Collapse
|
18
|
Motone K, Cardozo N, Nivala J. Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis. iScience 2021; 24:103032. [PMID: 34527891 PMCID: PMC8433247 DOI: 10.1016/j.isci.2021.103032] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.
Collapse
Affiliation(s)
- Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| |
Collapse
|
19
|
Ren R, Sun M, Goel P, Cai S, Kotov NA, Kuang H, Xu C, Ivanov AP, Edel JB. Single-Molecule Binding Assay Using Nanopores and Dimeric NP Conjugates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103067. [PMID: 34323323 DOI: 10.1002/adma.202103067] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/25/2021] [Indexed: 06/13/2023]
Abstract
The ability to measure biomarkers, both specifically and selectively at the single-molecule level in biological fluids, has the potential to transform the diagnosis, monitoring, and therapeutic intervention of diseases. The use of nanopores has been gaining prominence in this area, not only for sequencing but more recently in screening applications. The selectivity of nanopore sensing can be substantially improved with the use of labels, but substantial challenges remain, especially when trying to differentiate between bound from unbound targets. Here highly sensitive and selective molecular probes made from nanoparticles (NPs) that self-assemble and dimerize upon binding to a biological target are designed. It is shown that both single and paired NPs can be successfully resolved and detected at the single-molecule nanopore sensing and can be used for applications such as antigen/antibody detection and microRNA (miRNA) sequence analysis. It is expected that such technology will contribute significantly to developing highly sensitive and selective strategies for the diagnosis and screening of diseases without the need for sample processing or amplification while requiring minimal sample volume.
Collapse
Affiliation(s)
- Ren Ren
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Maozhong Sun
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Pratibha Goel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Shenglin Cai
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hua Kuang
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| |
Collapse
|
20
|
Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
Collapse
Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| |
Collapse
|
21
|
Nazarian R, Lee E, Siegel B, Kuo C, Acharya S, Schmidt J. Quantitative Measurements of Protein Volume and Concentration using Hydrogel-Backed Nanopores. ACS Sens 2021; 6:722-726. [PMID: 33703889 DOI: 10.1021/acssensors.1c00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate identification and quantification of proteins in solution using nanopores is technically challenging in part because of the large fraction of missed translocation events due to short event times and limitations of conventional current amplifiers. Previously, we have shown that a nanopore interfaced with a poly(ethylene glycol)-dimethacrylate hydrogel with an average mesh size of 3.1 nm significantly enhances the protein residence time within the pore, reducing the number of missed events. We used hydrogel-backed nanopores to sense unlabeled proteins as small as 5.5 kDa in size and 10 fM in concentration. We show that the frequency of protein translocation events linearly scales with bulk concentration over a wide range of concentrations and that unknown protein concentrations can be determined from an interpolation of the frequency-concentration curve with less than 10% error. Further, we show an iterative method to determine a protein volume accurately from measurement data for proteins with a diameter comparable to a nanopore diameter. Our measurements and analysis also suggest several competing mechanisms for the detection enhancement enabled by the presence of the hydrogel.
Collapse
Affiliation(s)
- Reyhaneh Nazarian
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Eric Lee
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Brian Siegel
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Chance Kuo
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Shiv Acharya
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Jacob Schmidt
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| |
Collapse
|
22
|
Maheshwaram SK, Sreenivasa K, Soni GV. Fingerprinting branches on supercoiled plasmid DNA using quartz nanocapillaries. NANOSCALE 2021; 13:320-331. [PMID: 33346295 DOI: 10.1039/d0nr06219g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA conformation, in particular its supercoiling, plays an important structural and functional role in gene accessibility as well as in DNA condensation. Enzyme driven changes of DNA plasmids between their linear, circular and supercoiled conformations control the level of condensation and DNA distal-site interactions. Much effort has been made to quantify the branched supercoiled state of DNA to understand its ubiquitous contribution to many biological functions, such as packaging, transcription, replication etc. Nanopore technology has proven to be an excellent label-free single-molecule method to investigate the conformations of the translocating DNA in terms of the current pulse readout. In this paper, we present a comprehensive study to detect different branched-supercoils on individual plasmid DNA molecules. Using a detailed event charge deficit (ECD) analysis of the translocating molecules, we reveal, for the first time, the distributions in size and the position of the plectoneme branches on the supercoiled plasmid. Additionally, this analysis also gives an independent measure of the effective nanopore length. Finally, we use our nanopore platform for measurement of enzyme-dependent linearization of these branched-supercoiled plasmids. By simultaneous measurement of both single-molecule DNA supercoiled conformations and enzyme-dependent bulk conformational changes, we establish nanopore sensing as a promising platform for an in-depth understanding of the structural landscapes of supercoiled DNA to decipher its functional role in different biological processes.
Collapse
|
23
|
Chau C, Radford SE, Hewitt EW, Actis P. Macromolecular Crowding Enhances the Detection of DNA and Proteins by a Solid-State Nanopore. NANO LETTERS 2020; 20:5553-5561. [PMID: 32559088 PMCID: PMC7357865 DOI: 10.1021/acs.nanolett.0c02246] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Indexed: 05/19/2023]
Abstract
Nanopore analysis of nucleic acid is now routine, but detection of proteins remains challenging. Here, we report the systematic characterization of the effect of macromolecular crowding on the detection sensitivity of a solid-state nanopore for circular and linearized DNA plasmids, globular proteins (β-galactosidase), and filamentous proteins (α-synuclein amyloid fibrils). We observe a remarkable ca. 1000-fold increase in the molecule count for the globular protein β-galactosidase and a 6-fold increase in peak amplitude for plasmid DNA under crowded conditions. We also demonstrate that macromolecular crowding facilitates the study of the topology of DNA plasmids and the characterization of amyloid fibril preparations with different length distributions. A remarkable feature of this method is its ease of use; it simply requires the addition of a macromolecular crowding agent to the electrolyte. We therefore envision that macromolecular crowding can be applied to many applications in the analysis of biomolecules by solid-state nanopores.
Collapse
Affiliation(s)
- Chalmers
C. Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric W. Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| |
Collapse
|
24
|
Huang G, Willems K, Bartelds M, van Dorpe P, Soskine M, Maglia G. Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores. NANO LETTERS 2020; 20:3819-3827. [PMID: 32271587 PMCID: PMC7227020 DOI: 10.1021/acs.nanolett.0c00877] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Indexed: 05/19/2023]
Abstract
Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.
Collapse
Affiliation(s)
- Gang Huang
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
- imec, Kapeldreef 75, 3001 Leuven, Belgium
| | - Mart Bartelds
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol van Dorpe
- imec, Kapeldreef 75, 3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Misha Soskine
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| |
Collapse
|
25
|
Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
Collapse
|
26
|
Lee K, Kang JH, Kim HM, Ahn J, Lim H, Lee J, Jeon WJ, Lee JH, Kim KB. Direct electrophoretic microRNA preparation from clinical samples using nanofilter membrane. NANO CONVERGENCE 2020; 7:1. [PMID: 31930443 PMCID: PMC6955385 DOI: 10.1186/s40580-019-0212-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/08/2019] [Indexed: 05/17/2023]
Abstract
A method to directly collect negatively charged nucleic acids, such as DNA and RNA, in the biosamples simply by applying an electric field in between the sample and collection buffer separated by the nanofilter membrane is proposed. The nanofilter membrane was made of low-stress silicon nitride with a thickness of 100 nm, and multiple pores were perforated in a highly arranged pattern using nanoimprint technology with a pore size of 200 nm and a pore density of 7.22 × 108/cm2. The electrophoretic transport of hsa-mir-93-5p across the membrane was confirmed in pure microRNA (miRNA) mimic solution using quantitative reverse transcription-polymerase chain reactions (qRT-PCR). Consistency of the collected miRNA quantity, stability of the system during the experiment, and yield and purity of the prepared sample were discussed in detail to validate the effectiveness of the electrical protocol. Finally, in order to check the applicability of this method to clinical samples, liquid biopsy process was demonstrated by evaluating the miRNA levels in sera of hepatocellular carcinoma patients and healthy controls. This efficient system proposed a simple, physical idea in preparation of nucleic acid from biosamples, and demonstrated its compatibility to biological downstream applications such as qRT-PCR as the conventional nucleic acid extraction protocols.
Collapse
Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hyun Kang
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junhyoung Ahn
- Department of Nano Manufacturing Technology, Nano Convergence Mechanical Systems Research Division, Korea Institute of Machinery & Materials (KIMM), Daejeon, 34103, Republic of Korea
| | - Hyungjun Lim
- Department of Nano Manufacturing Technology, Nano Convergence Mechanical Systems Research Division, Korea Institute of Machinery & Materials (KIMM), Daejeon, 34103, Republic of Korea
- Department of Nanomechatronics, University of Science & Technology, Daejeon, 34113, Republic of Korea
| | - JaeJong Lee
- Department of Nano Manufacturing Technology, Nano Convergence Mechanical Systems Research Division, Korea Institute of Machinery & Materials (KIMM), Daejeon, 34103, Republic of Korea
- Department of Nanomechatronics, University of Science & Technology, Daejeon, 34113, Republic of Korea
| | - Wan-Jin Jeon
- Heimbiotek Inc., Seongnam, Gyeonggi-do, 13486, Republic of Korea
| | - Jae-Hoon Lee
- Heimbiotek Inc., Seongnam, Gyeonggi-do, 13486, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
27
|
Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
Collapse
Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| |
Collapse
|
28
|
Wang Z, Liu Y, Yu L, Li Y, Qian G, Chang S. Nanopipettes: a potential tool for DNA detection. Analyst 2019; 144:5037-5047. [PMID: 31290857 DOI: 10.1039/c9an00633h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.
Collapse
Affiliation(s)
- Zhe Wang
- The State Key Laboratory of Refractories and Metallurgy, and Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, China.
| | | | | | | | | | | |
Collapse
|
29
|
Sun H, Yao F, Kang XF. Nanopore biphasic-pulse biosensor. Biosens Bioelectron 2019; 146:111740. [PMID: 31586766 DOI: 10.1016/j.bios.2019.111740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022]
Abstract
Nanopores as artificial biomimetic nanodevices are of great importance for their applications in biosensing, nanomedicine and bioelectronics. However, it remains a challenge to detect small biomolecules especially small-sized proteins with high sensitivity and selectivity. In the article, we report a simple and efficient method for small-sized protein detection by constructing biphasic-pulse nanopore biosensor. Unlike the traditional resistive pulse sensing, the biphasic-pulse event can provide unique and abundant fingerprint information. Although the nanopore biphasic-pulse electrical signal is originated from both the molecular exclusion electrical resistance and the surface-charged effect of confined molecule, its frequency and amplitude of the waveform can be adjusted by pH, applied potential and salt concentration. Based on the frequency of the biphasic pulse, nanomolar concentration of proteins could be specifically detected and the limit of detection is 1.2 nM. In addition, the biphasic-pulse nanopore shows well discrimination in similar-sized protein detection and its signal generation is highly reproducible. The nanopore biphasic-pulse biosensor should have broad applications as a new generation of powerful single-molecule device.
Collapse
Affiliation(s)
- Hong Sun
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China.
| |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Qi Chen
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
| | - Zewen Liu
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
31
|
Si W, Zhang Y, Wu G, Kan Y, Zhang Y, Sha J, Chen Y. Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900036. [PMID: 30848871 DOI: 10.1002/smll.201900036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/24/2019] [Indexed: 05/03/2023]
Abstract
The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.
Collapse
Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yin Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yajing Kan
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yan Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| |
Collapse
|
32
|
Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
Collapse
Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| |
Collapse
|
33
|
Wang D, Xu X, Zhou Y, Li H, Qi G, Hu P, Jin Y. Short-chain oligonucleotide detection by glass nanopore using targeting-induced DNA tetrahedron deformation as signal amplifier. Anal Chim Acta 2019; 1063:57-63. [PMID: 30967186 DOI: 10.1016/j.aca.2019.02.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 01/22/2023]
Abstract
Glass capillary nanopore has been developed as a promising sensing platform for bioassay with single-molecule resolution. Although the diameter of glass capillary nanopore can be easily tuned, direct event-readouts of small biomacromolecules, like short-chain oligonucleotide fragments (within ∼20 nucleotides) remain great challenge, which limited by the configuration of the conical-shaped nanopore and the instrumental temporal resolution. Here, we exploit a smart strategy for glass nanopore detection of short-chain oligonucleotides by using relatively big-sized tetrahedral DNA nanostructures as a signal amplifier, which can amplify the signals and retard the translocation speed meanwhile. The tetrahedral DNA nanostructure with a hairpin loop sequence in one edge, undergoes a shape transformation upon the complementary combination of the target oligonucleotides, in which the presence of short-chain target oligonucleotide can be readout due to obvious variation in amplitude of ion current pulse that caused by volume change of the DNA tetrahedral. Therefore, this strategy is promising for extending glass nanopore sensing platform for sensitive detection of short-chain oligonucleotides.
Collapse
Affiliation(s)
- Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiaolong Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Ya Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Hu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
34
|
Si W, Yang H, Sha J, Zhang Y, Chen Y. Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores. Electrophoresis 2019; 40:2117-2124. [PMID: 30779188 DOI: 10.1002/elps.201800537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.
Collapse
Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Haojie Yang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yin Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| |
Collapse
|
35
|
Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
Collapse
Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| |
Collapse
|
36
|
Fraccari RL, Carminati M, Piantanida G, Leontidou T, Ferrari G, Albrecht T. High-bandwidth detection of short DNA in nanopipettes. Faraday Discuss 2018; 193:459-470. [PMID: 27711887 DOI: 10.1039/c6fd00109b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. The ease of fabrication, favourable wetting properties and low capacitance are some of the inherent advantages, for example compared to more conventional, silicon-based nanopore chips. Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. The electronics design has now been refined to include more sophisticated control features, such as integrated bias reversal and other features. Here, we exploit these capabilities and probe the translocation of short dsDNA in the 100 bp range, in different electrolytes. Single-stranded (ss) DNA of similar length are in use as capture probes, so label-free detection of their ds counterparts could therefore be of relevance in disease diagnostics.
Collapse
Affiliation(s)
- Raquel L Fraccari
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Marco Carminati
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Giacomo Piantanida
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tina Leontidou
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Giorgio Ferrari
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| |
Collapse
|
37
|
Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
Collapse
Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| |
Collapse
|
38
|
Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore. Nat Commun 2018; 9:966. [PMID: 29511176 PMCID: PMC5840376 DOI: 10.1038/s41467-018-03418-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
Collapse
|
39
|
Lee K, Lee H, Lee SH, Kim HM, Kim KB, Kim SJ. Enhancing the sensitivity of DNA detection by structurally modified solid-state nanopore. NANOSCALE 2017; 9:18012-18021. [PMID: 29131223 DOI: 10.1039/c7nr05840c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Solid-state nanopore is an ionic current-based biosensing platform, which would be a top candidate for next-generation DNA sequencing and a high-throughput drug-screening tool at single-molecular-scale resolution. There have been several approaches to enhance the sensitivity and reliability of biomolecule detection using the nanopores particularly in two aspects: signal-to-noise ratio (SNR) and translocation dwell time. In this study, an additional nano-well of 100-150 nm diameter and the aspect ratio of ∼5 called 'guide structure' was inserted in conventional silicon-substrate nanopore device to increase both SNR and dwell time. First, the magnitude of signals (conductance drop (ΔG)) increased 2.5 times under applied voltage of 300 mV through the guide-inserted nanopore compared to the conventional SiN/Si nanopore in the same condition. Finite element simulation was conducted to figure out the origin of ΔG modification, which showed that the guide structure produced high ΔG due to the compartmental limitation of ion transports through the guide to the sensing nanopore. Second, the translocation velocity decreased in the guide-inserted structure to a maximum of 20% of the velocity in the conventional device at 300 mV. Electroosmotic drag formed inside the guide structure, when directly applied to the remaining segment of translocating DNA molecules in cis chamber, affected the DNA translocation velocity. This study is the first experimental report on the effect of the geometrical confinement to a remnant DNA on both SNR and dwell time of nanopore translocations.
Collapse
Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea.
| | | | | | | | | | | |
Collapse
|
40
|
Lam J, Lutsko JF. Solute particle near a nanopore: influence of size and surface properties on the solvent-mediated forces. NANOSCALE 2017; 9:17099-17108. [PMID: 29087410 DOI: 10.1039/c7nr07218j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanoscopic pores are used in various systems to attract nanoparticles. In general the behaviour is a result of two types of interactions: the material specific affinity and the solvent-mediated influence also called the depletion force. The latter is more universal but also much more complex to understand since it requires modeling both the nanoparticle and the solvent. Here, we employed classical density functional theory to determine the forces acting on a nanoparticle near a nanoscopic pore as a function of its hydrophobicity and its size. A simple capillary model is constructed to predict those depletion forces for various surface properties. For a nanoscopic pore, complexity arises from both the specific geometry and the fact that hydrophobic pores are not necessarily filled with liquid. Taking all of these effects into account and including electrostatic effects, we establish a phase diagram describing the entrance and the rejection of the nanoparticle from the pore.
Collapse
Affiliation(s)
- Julien Lam
- Center for Nonlinear Phenomena and Complex Systems, Code Postal 231, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - James F Lutsko
- Center for Nonlinear Phenomena and Complex Systems, Code Postal 231, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium.
| |
Collapse
|
41
|
Huang G, Willems K, Soskine M, Wloka C, Maglia G. Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores. Nat Commun 2017; 8:935. [PMID: 29038539 PMCID: PMC5715100 DOI: 10.1038/s41467-017-01006-4] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Biological nanopores are nanoscale sensors employed for high-throughput, low-cost, and long read-length DNA sequencing applications. The analysis and sequencing of proteins, however, is complicated by their folded structure and non-uniform charge. Here we show that an electro-osmotic flow through Fragaceatoxin C (FraC) nanopores can be engineered to allow the entry of polypeptides at a fixed potential regardless of the charge composition of the polypeptide. We further use the nanopore currents to discriminate peptide and protein biomarkers from 25 kDa down to 1.2 kDa including polypeptides differing by one amino acid. On the road to nanopore proteomics, our findings represent a rationale for amino-acid analysis of folded and unfolded polypeptides with nanopores. Biological nanopore–based protein sequencing and recognition is challenging due to the folded structure or non-uniform charge of peptides. Here the authors show that engineered FraC nanopores can overcome these problems and recognize biomarkers in the form of oligopeptides, polypeptides and folded proteins.
Collapse
Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Kherim Willems
- KU Leuven Department of Chemistry, Celestijnenlaan 200G, 3001, Leuven, Belgium.,Imec, Kapeldreef 75, 3001, Leuven, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
42
|
Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 PMCID: PMC11274829 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
Collapse
Affiliation(s)
- Amy E. Chavis
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph W. F. Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
43
|
Wang S, Zhou Z, Zhao Z, Zhang H, Haque F, Guo P. Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states. Biomaterials 2017; 126:10-17. [PMID: 28237908 PMCID: PMC5421631 DOI: 10.1016/j.biomaterials.2017.01.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
Abstract
Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the passage of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures. Utilizing single channel conductance assay and optical single molecule imaging, we observed translocation of peptides and quantitatively analyzed the dynamics of peptide oligomeric states in real-time at single molecule level. The oxidative and the reduced states of peptides were clearly differentiated based on their characteristic electronic signatures. A similar Gibbs free energy (ΔG0) was obtained when different concentrations of substrates were applied, suggesting that the use of SPP1 nanopore for real-time quantification of peptide oligomeric states is feasible. With the intrinsic nature of size and conjugation amenability, the SPP1 nanopore has the potential for development into a tool for the quantification of peptide and protein structures in real time.
Collapse
Affiliation(s)
- Shaoying Wang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhi Zhou
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zhengyi Zhao
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Hui Zhang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Farzin Haque
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.
| |
Collapse
|
44
|
Lin X, Ivanov AP, Edel JB. Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles. Chem Sci 2017; 8:3905-3912. [PMID: 28626560 PMCID: PMC5465561 DOI: 10.1039/c7sc00415j] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023] Open
Abstract
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
Collapse
Affiliation(s)
- Xiaoyan Lin
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Aleksandar P Ivanov
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| |
Collapse
|
45
|
Barati Farimani A, Heiranian M, Min K, Aluru NR. Antibody Subclass Detection Using Graphene Nanopores. J Phys Chem Lett 2017; 8:1670-1676. [PMID: 28325049 DOI: 10.1021/acs.jpclett.7b00385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Solid-state nanopores are promising for label-free protein detection. The large thickness, ranging from several tens of nanometers to micrometers and larger, of solid-state nanopores prohibits atomic-scale scanning or interrogation of proteins. Here, a single-atom thick graphene nanopore is shown to be highly capable of sensing and discriminating between different subclasses of IgG antibodies despite their minor and subtle variation in atomic structure. Extensive molecular dynamics (MD) simulations, rigorous statistical analysis with a total aggregate simulation time of 2.7 μs, supervised machine learning (ML), and classification techniques are employed to distinguish IgG2 from IgG3. The water flux and ionic current during IgG translocation reveal distinct clusters for IgG subclasses facilitating an additional recognition mechanism. In addition, the histogram of ionic current for each segment of IgG can provide high-resolution spatial detection. Our results show that nanoporous graphene can be used to detect and distinguish antibody subclasses with good accuracy.
Collapse
Affiliation(s)
- Amir Barati Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Mohammad Heiranian
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Kyoungmin Min
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| |
Collapse
|
46
|
Bulushev RD, Marion S, Petrova E, Davis SJ, Maerkl SJ, Radenovic A. Single Molecule Localization and Discrimination of DNA-Protein Complexes by Controlled Translocation Through Nanocapillaries. NANO LETTERS 2016; 16:7882-7890. [PMID: 27960483 DOI: 10.1021/acs.nanolett.6b04165] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Through the use of optical tweezers we performed controlled translocations of DNA-protein complexes through nanocapillaries. We used RNA polymerase (RNAP) with two binding sites on a 7.2 kbp DNA fragment and a dCas9 protein tailored to have five binding sites on λ-DNA (48.5 kbp). Measured localization of binding sites showed a shift from the expected positions on the DNA that we explained using both analytical fitting and a stochastic model. From the measured force versus stage curves we extracted the nonequilibrium work done during the translocation of a DNA-protein complex and used it to obtain an estimate of the effective charge of the complex. In combination with conductivity measurements, we provided a proof of concept for discrimination between different DNA-protein complexes simultaneous to the localization of their binding sites.
Collapse
Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenička cesta 46, HR-10000 Zagreb, Croatia
| | - Ekaterina Petrova
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Davis
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sebastian J Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| |
Collapse
|
47
|
Hsu WL, Daiguji H. Manipulation of Protein Translocation through Nanopores by Flow Field Control and Application to Nanopore Sensors. Anal Chem 2016; 88:9251-8. [PMID: 27571138 DOI: 10.1021/acs.analchem.6b02513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.
Collapse
Affiliation(s)
- Wei-Lun Hsu
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
| |
Collapse
|
48
|
Ji Z, Wang S, Zhao Z, Zhou Z, Haque F, Guo P. Fingerprinting of Peptides with a Large Channel of Bacteriophage Phi29 DNA Packaging Motor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4572-8. [PMID: 27435806 PMCID: PMC5166430 DOI: 10.1002/smll.201601157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/16/2016] [Indexed: 05/27/2023]
Abstract
Nanopore technology has become a highly sensitive and powerful tool for single molecule sensing of chemicals and biopolymers. Protein pores have the advantages of size amenability, channel homogeneity, and fabrication reproducibility. But most well-studied protein pores for sensing are too small for passage of peptide analytes that are typically a few nanometers in dimension. The funnel-shaped channel of bacteriophage phi29 DNA packaging motor has previously been inserted into a lipid membrane to serve as a larger pore with a narrowest N-terminal constriction of 3.6 nm and a wider C-terminal end of 6 nm. Here, the utility of phi29 motor channel for fingerprinting of various peptides using single molecule electrophysiological assays is reported. The translocation of peptides is proved unequivocally by single molecule fluorescence imaging. Current blockage percentage and distinctive current signatures are used to distinguish peptides with high confidence. Each peptide generated one or two distinct current blockage peaks, serving as typical fingerprint for each peptide. The oligomeric states of peptides can also be studied in real time at single molecule level. The results demonstrate the potential for further development of phi29 motor channel for detection of disease-associated peptide biomarkers.
Collapse
|
49
|
Zweifel LP, Shorubalko I, Lim RYH. Helium Scanning Transmission Ion Microscopy and Electrical Characterization of Glass Nanocapillaries with Reproducible Tip Geometries. ACS NANO 2016; 10:1918-1925. [PMID: 26783633 DOI: 10.1021/acsnano.5b05754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nanopores fabricated from glass microcapillaries are used in applications ranging from scanning ion conductance microscopy to single-molecule detection. Still, evaluating the nanocapillary tip by a noninvasive means remains challenging. For instance, electron microscopy characterization techniques can charge, heat, and contaminate the glass surface and typically require conductive coatings that influence the final tip geometry. Per contra, electrical characterization by the means of ion current through the capillary lumen provides only indirect geometrical details of the tips. Here, we show that helium scanning transmission ion microscopy provides a nondestructive and precise determination of glass nanocapillary tip geometries. This enables the reproducible fabrication of axially asymmetric blunt, bullet, and hourglass-shaped tips with opening diameters from 20 to 400 nm by laser-assisted pulling. Accordingly, this allows for an evaluation of how tip shape, pore diameter, and opening angle impact ionic current rectification behavior and the translocation of single molecules. Our analysis shows that current drops and translocation dwell times are dominated by the pore diameter and opening angles regardless of nanocapillary tip shape.
Collapse
Affiliation(s)
- Ludovit P Zweifel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel , 4056 Basel, Switzerland
| | - Ivan Shorubalko
- Laboratory for Reliability Science and Technology, EMPA, Swiss Federal Laboratories for Materials Science and Technology , 8600 Dübendorf, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel , 4056 Basel, Switzerland
| |
Collapse
|
50
|
Hu ZL, Cao C, Wang HF, Yan BY. Alkyl detection facilitated by a DNA conjugate with an α-hemolysin nanopore. RSC Adv 2016. [DOI: 10.1039/c5ra20425a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel α-hemolysin nanopore (α-HL) based strategy for the detection of an alkyl linker at the single-molecule level.
Collapse
Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials & Department of Chemistry
- East China University of Sciences and Technology
- Shanghai
- P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials & Department of Chemistry
- East China University of Sciences and Technology
- Shanghai
- P. R. China
| | - Hui-Feng Wang
- East China University of Sciences and Technology
- Shanghai
- P. R. China
| | - Bing-Yong Yan
- School of Information Science and Engineering
- East China University of Sciences and Technology
- Shanghai
- P. R. China
| |
Collapse
|