1
|
Zhang Y, Yi Y, Li Z, Zhou K, Liu L, Wu HC. Peptide sequencing based on host-guest interaction-assisted nanopore sensing. Nat Methods 2024; 21:102-109. [PMID: 37957431 DOI: 10.1038/s41592-023-02095-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Direct protein sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose an alternative method for peptide sequencing based on enzymatic cleavage and host-guest interaction-assisted nanopore sensing. We serendipitously discovered that the identity of any proteinogenic amino acid in a particular position of a phenylalanine-containing peptide could be determined via current blockage during translocation of the peptide through α-hemolysin nanopores in the presence of cucurbit[7]uril. Building upon this, we further present a proof-of-concept demonstration of peptide sequencing by sequentially cleaving off amino acids from C terminus of a peptide with carboxypeptidases, and then determining their identities and sequence with a peptide probe in nanopore. With future optimization, our results point to a different way of nanopore-based protein sequencing.
Collapse
Affiliation(s)
- Yun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yakun Yi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
2
|
Li J, Li M, Zhang K, Hu L, Li D. High-Performance Integrated Iontronic Circuits Based on Single Nano/Microchannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2208079. [PMID: 36869414 DOI: 10.1002/smll.202208079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/13/2023] [Indexed: 06/02/2023]
Abstract
Recently, artificial channel-based ionic diodes and transistors are extensively studied to mimic biological systems. Most of them are constructed vertically and are challenging to be further integrated. Several examples of ionic circuits with horizontal ionic diodes are reported. However, they generally require nanoscale channel sizes to meet the demand for ion-selectivity, resulting in low current output and restricting potential applications. In this paper, a novel ionic diode is developed based on multiple-layer polyelectrolyte nanochannel network membranes. Both bipolar and unipolar ionic diodes can be achieved by simply switching the modification solution. Ionic diodes with a high rectification ratio of ≈226 are achieved in single channels with the largest channel size of 2.5 µm. This design can significantly reduce the channel size requirement and improve the output current level of ionic devices. The high-performance ionic diode with a horizontal structure enables the integration of advanced iontronic circuits. Ionic transistors, logic gates, and rectifiers are fabricated on a single chip and demonstrated for current rectification. Furthermore, the excellent current rectification ratio and the high output current of the on-chip ionic devices highlight the promise of the ionic diode as a component of complex iontronic systems for practical applications.
Collapse
Affiliation(s)
- Jun Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Mengqi Li
- Department of Marine Engineering, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Kaiping Zhang
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Lide Hu
- Department of Marine Engineering, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Dongqing Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| |
Collapse
|
3
|
Hu G, Yan H, Xi G, Gao Z, Wu Z, Lu Z, Tu J. Nanopore sensors for single molecular protein detection: Research progress based on computer simulations. IET Nanobiotechnol 2023; 17:257-268. [PMID: 36924083 DOI: 10.1049/nbt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.
Collapse
Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| |
Collapse
|
4
|
Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
Collapse
Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
| |
Collapse
|
5
|
Li J, Zhang K, Li D. pH-Regulated Ionic Diode Based on an Asymmetric Shaped Multiple-Layer Polymer Membrane. Anal Chem 2023; 95:1419-1427. [PMID: 36534674 DOI: 10.1021/acs.analchem.2c04369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Smart artificial ion channels with tunable properties have wide applications in many fields to achieve ion transport manipulation. Most reported artificial ions are constructed with vertical structures, limiting the further integration of ionic diodes into complex iontronic systems. Inspired by the asymmetric concentration polarization induced by the asymmetric geometry of nanochannels, a novel method is developed to construct horizontally arranged and pH-regulated ionic diodes in nanofluidic chips by self-assembling pH-responsive polymers. The effects of the fabrication and operation parameters on the performance of the ionic diode are systematically investigated. The current rectification ratio of the ionic diode can be modulated flexibly by regulating the pH conditions of the working fluid. An ionic diode bridge circuit for rectifying alternating current signals is built in a single nanofluidic chip and demonstrated, highlighting the feasibility of the ionic diode for complex iontronic system integration. The method presented in this paper provides a promising platform for the development of smart nanofluidic iontronic devices with widespread applicability in biological analysis, sensing, and logic computing.
Collapse
Affiliation(s)
- Jun Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Kaiping Zhang
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| | - Dongqing Li
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, OntarioN2L 3G1, Canada
| |
Collapse
|
6
|
Shrestha B, Tang L, Hood RL. Nanotechnology for Personalized Medicine. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
7
|
Mittal S, Manna S, Pathak B. Machine Learning Prediction of the Transmission Function for Protein Sequencing with Graphene Nanoslit. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51645-51655. [PMID: 36374991 DOI: 10.1021/acsami.2c13405] [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: 06/16/2023]
Abstract
Protein sequencing has rapidly changed the landscape of healthcare and life science by accelerating the growth of diagnostics and personalized medicines for a variety of fatal diseases. Next-generation nanopore/nanoslit sequencing is promising to achieve single-molecule resolution with chromosome-size-long readability. However, due to inherent complexity, high-throughput sequencing of all 20 amino acids demands different approaches. Aiming to accelerate the detection of amino acids, a general machine learning (ML) method has been developed for quick and accurate prediction of the transmission function for amino acid sequencing. Among the utilized ML models, the XGBoost regression model is found to be the most effective algorithm for fast prediction of the transmission function with a very low test root-mean-square error (RMSE ∼0.05). In addition, using the random forest ML classification technique, we are able to classify the neutral amino acids with a prediction accuracy of 100%. Therefore, our approach is an initiative for the prediction of the transmission function through ML and can provide a platform for the quick identification of amino acids with high accuracy.
Collapse
Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Souvik Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| |
Collapse
|
8
|
Liu L, Luo C, Zhang J, He X, Shen Y, Yan B, Huang Y, Xia F, Jiang L. Synergistic Effect of Bio-Inspired Nanochannels: Hydrophilic DNA Probes at Inner Wall and Hydrophobic Coating at Outer Surface for Highly Sensitive Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201925. [PMID: 35980948 DOI: 10.1002/smll.202201925] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/16/2022] [Indexed: 06/15/2023]
Abstract
During the past few decades, bio-inspired nanochannels have been well developed and applied in biosensing, energy transfer, separation, and so on. Here, inspired by the synergistic effect of biological nanopores, biomimetic solid-state nanochannels with hydrophilic DNA probes at the inner wall (DNA@IWHydrophilic ) and hydrophobic coating at the outer surface (None@OSHydrophobic ) are designed. To demonstrate their prompted sensing properties, Hg2+ and its specific probe are selected as target and hydrophilic DNA probes, respectively. Compared with the traditional solid-state nanochannels with hydrophilic probes distributed on both the inner wall and outer surface, the nanochannels with DNA@IWHydrophilic +None@OSHydrophobic significantly decrease the limit of detection (LOD) by 105 -fold. The obvious improvement of sensitivity (with LOD of 1 nM) is attributed to the synergistic effect: None@OSHydrophobic results in the nanochannel's effective diameter decrease and DNA@IWHydrophilic induces a specific sensing target. Meanwhile, nanomolar detection of Hg2+ in human serum and in vivo fish muscle are achieved. Through molecular dynamics simulation, the synergistic effect can be confirmed by ion fluxes increasement; the relative carbon nanotube increases from 135.64% to 135.84%. This work improves the understanding of nanochannels' synergistic effect and provides a significant insight for nanochannels with improved sensitivity.
Collapse
Affiliation(s)
- Lingxiao Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Cihui Luo
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, P. R. China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, P. R. China
| | - Ying Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Bing Yan
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Yu Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry and Environment, Beihang University, Beijing, 100191, P. R. China
| |
Collapse
|
9
|
Zollo G, Civitarese T. Ab Initio Properties of Hybrid Cove-Edged Graphene Nanoribbons as Metallic Electrodes for Peptide Sequencing via Transverse Tunneling Current. ACS OMEGA 2022; 7:25164-25170. [PMID: 35910163 PMCID: PMC9330076 DOI: 10.1021/acsomega.2c01917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recently synthesized metallic cove-edged graphene nanoribbons are considered for use as one-dimensional (1D) electrodes for ideal atomistically resolved recognition of amino acids. To this purpose a narrow nanogap device is considered, and the transversal tunneling current flowing across it is calculated during the translocation of a model Gly homopeptide using the nonequilibrium Green function scheme, based on density functional theory. We show that the signal collected from the metallic spin states is characterized by a double peak per residue in analogy with the results obtained with 1D graphene nanoribbon template electrodes. The presented results pave the way for experimentally feasible atomistically resolved tunneling current recognition using metallic edge engineered graphene electrodes obtained by bottom-up fabrication strategies.
Collapse
|
10
|
Wang X, Stevens KC, Ting JM, Marras AE, Rezvan G, Wei X, Taheri-Qazvini N, Tirrell MV, Liu C. Translocation Behaviors of Synthetic Polyelectrolytes through Alpha-Hemolysin (α-HL) and Mycobacterium smegmatis Porin A (MspA) Nanopores. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2022; 169:057510. [PMID: 35599744 PMCID: PMC9121822 DOI: 10.1149/1945-7111/ac6c55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNAs have been used as probes for nanopore sensing of noncharged biomacromolecules due to its negative phosphate backbone. Inspired by this, we explored the potential of diblock synthetic polyelectrolytes as more flexible and inexpensive nanopore sensing probes by investigating translocation behaviors of PEO-b-PSS and PEO-b-PVBTMA through commonly used alpha-hemolysin (α-HL) and Mycobacterium smegmatis porin A (MspA) nanopores. Translocation recordings in different configurations of pore orientation and testing voltage indicated efficient PEO-b-PSS translocations through α-HL and PEO-b-PVBTMA translocations through MspA. This work provides insight into synthetic polyelectrolyte-based probes to expand probe selection and flexibility for nanopore sensing.
Collapse
Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kaden C. Stevens
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey M. Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander E. Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| |
Collapse
|
11
|
Review of the use of nanodevices to detect single molecules. Anal Biochem 2022; 654:114645. [DOI: 10.1016/j.ab.2022.114645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
|
12
|
Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| |
Collapse
|
13
|
Shrestha B, Tang L, Hood RL. Nanotechnology for Personalized Medicine. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_18-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
14
|
Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
Collapse
Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| |
Collapse
|
15
|
Liu SC, Xie BK, Zhong CB, Wang J, Ying YL, Long YT. An advanced optical-electrochemical nanopore measurement system for single-molecule analysis. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:121301. [PMID: 34972456 DOI: 10.1063/5.0067185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Nanopore measurement has advanced in single-molecule analysis by providing a transient time and confined space window that only allows one interested molecule to exist. By optimization and integration of the electrical and optical analysis strategies in this transient window, the acquisition of comprehensive information could be achieved to resolve the intrinsic properties and heterogeneity of a single molecule. In this work, we present a roadmap to build a unified optical and electrochemical synchronous measurement platform for the research of a single molecule. We design a low-cost ultralow-current amplifier with low noise and high-bandwidth to measure the ionic current events as a single molecule translocates through a nanopore and combine a multi-functional optical system to implement the acquisition of the fluorescence, scattering spectrum, and photocurrent intensity of single molecule events in a nanopore confined space. Our system is a unified and unique platform for the protein nanopore, the solid-state nanopore, and the glass capillary nanopore, which has advantages in the comprehensive research of nanopore single-molecule techniques.
Collapse
Affiliation(s)
- Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Bao-Kang Xie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jia Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| |
Collapse
|
16
|
Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. NANOSCALE 2021; 13:15352-15361. [PMID: 34498657 DOI: 10.1039/d1nr04492c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise amino acid identification.
Collapse
Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Haojie Yang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| |
Collapse
|
17
|
Tsutsui M, Takaai T, Yokota K, Kawai T, Washio T. Deep Learning-Enhanced Nanopore Sensing of Single-Nanoparticle Translocation Dynamics. SMALL METHODS 2021; 5:e2100191. [PMID: 34928002 DOI: 10.1002/smtd.202100191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/17/2021] [Indexed: 06/14/2023]
Abstract
Noise is ubiquitous in real space that hinders detection of minute yet important signals in electrical sensors. Here, the authors report on a deep learning approach for denoising ionic current in resistive pulse sensing. Electrophoretically-driven translocation motions of single-nanoparticles in a nano-corrugated nanopore are detected. The noise is reduced by a convolutional auto-encoding neural network, designed to iteratively compare and minimize differences between a pair of waveforms via a gradient descent optimization. This denoising in a high-dimensional feature space is demonstrated to allow detection of the corrugation-derived wavy signals that cannot be identified in the raw curves nor after digital processing in frequency domains under the given noise floor, thereby enabled in-situ tracking to electrokinetic analysis of fast-moving single- and double-nanoparticles. The ability of the unlabeled learning to remove noise without compromising temporal resolution may be useful in solid-state nanopore sensing of protein structure and polynucleotide sequence.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Takayuki Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| |
Collapse
|
18
|
Lenhart B, Wei X, Watson B, Wang X, Zhang Z, Li C, Moss M, Liu C. In Vitro Biosensing of β-Amyloid Peptide Aggregation Dynamics using a Biological Nanopore. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 338:129863. [PMID: 33927481 PMCID: PMC8078859 DOI: 10.1016/j.snb.2021.129863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Alzheimer's disease and other neurodegenerative disorders are becoming more prevalent as advances in technology and medicine increase living standards and life expectancy. Alzheimer's disease is thought to initiate development early in the patient's life and progresses continuously into old age. This process is characterized molecularly by the amyloid hypothesis, which asserts that self-aggregating amyloid peptides are core to the pathophysiology in Alzheimer's progression. Precise quantification of amyloid peptides in human bodily fluid samples (i.e. cerebrospinal fluid, blood) may inform diagnosis and prognosis, and has been studied using established biosensing technologies like liquid chromatography, mass spectrometry, and immunoassays. However, existing methods are challenged to provide single molecule, quantitative analysis of the disease-causing aggregation process. Ultra-sensitive nanopore biosensors can step in to fill this role as a dynamic mapping tool. The work in this paper establishes characteristic signals of β-amyloid 40 monomers, oligomers, and soluble aggregates, as well as a proof-of-concept foundation where a biological nanopore biosensor is used to monitor the extent of in vitro β-amyloid 40 peptide aggregation at the single molecule level. This foundation allows for future work to expand in drug screening, diagnostics, and aggregation dynamic experiments.
Collapse
Affiliation(s)
- Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Brittany Watson
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chenzhong Li
- Center for Cellular and Molecular Diagnostics, Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Melissa Moss
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
19
|
Hossain JA, Kim B. Scale Effect on Simple Liquid Transport through a Nanoporous Graphene Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6498-6509. [PMID: 34018744 DOI: 10.1021/acs.langmuir.1c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The transport mechanism of a simple liquid through nanoporous graphene membranes (NPGMs) with pores of various diameters has been explored by utilizing nonequilibrium molecular dynamics (NEMD) simulation. The flow is initiated using a pressure-driven flow mechanism that moves the specular reflection wall at a constant velocity. Both the local density peak near the membrane and the pressure drop are dependent on the pore diameter. For accurate calculation of the velocity profile inside the nanopore, we implemented three boundary approaches and local nanoscale variants to see the effect of these factors on the nature of the nanoscale flow. We found an optimized definition of the pore boundary, which minimizes the deviation between MD results and slip-viscosity-modified Sampson's prediction for nanopores of various diameters. Additionally, we observed that with decreasing pore size, the pore center velocity increases, as does the slip velocity, which we attributed to van der Waals interaction between the liquid and wall atoms inside the nanopore. However, the effects of slip velocity, interfacial viscosity, and pore boundary decay exponentially with increasing pore diameter because of the dominance of van der Waals repulsive forces at the molecular level.
Collapse
Affiliation(s)
- Jaber Al Hossain
- School of Mechanical Engineering, University of Ulsan, Daehak-ro 93, Nam-gu, Ulsan 680-749, South Korea
| | - BoHung Kim
- School of Mechanical Engineering, University of Ulsan, Daehak-ro 93, Nam-gu, Ulsan 680-749, South Korea
| |
Collapse
|
20
|
Wei X, Zhang Z, Wang X, Lenhart B, Gambarini R, Gray J, Liu C. Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore. NANOTECHNOLOGY AND PRECISION ENGINEERING 2021; 3:2-8. [PMID: 33786424 PMCID: PMC8006565 DOI: 10.1016/j.npe.2019.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various molecules. However, the effect of several electrochemical factors on the host-guest interactions in nanopore still remains unknown. Here, we systematically studied host-guest interactions, especially oscillation of DNA-azide adamantane@cucurbit[6] in α-Hemolysin nanopore under varying pH, concentration of electrolytes and counterions (Li+, Na+, K+). Our results indicate correlations between the change of pH and the duration of the oscillation signal. In addition, the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals, and even the integrity of the protein nanopore. This study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.
Collapse
Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Roberto Gambarini
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jonathan Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
21
|
Tang Z, Dong M, He X, Guan W. On Stochastic Reduction in Laser-Assisted Dielectric Breakdown for Programmable Nanopore Fabrication. ACS APPLIED MATERIALS & INTERFACES 2021; 13:13383-13391. [PMID: 33705089 DOI: 10.1021/acsami.0c23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The controlled dielectric breakdown emerged as a promising alternative toward accessible solid-state nanopore fabrication. Several prior studies have shown that laser-assisted dielectric breakdown could help control the nanopore position and reduce the possibility of forming multiple pores. Here, we developed a physical model to estimate the probability of forming a single nanopore under different combinations of the laser power and the electric field. This model relies on the material- and experiment-specific parameters: the Weibull statistical parameters and the laser-induced photothermal etching rate. Both the model and our experimental data suggest that a combination of a high laser power and a low electric field is statistically favorable for forming a single nanopore at a programmed location. While this model relies on experiment-specific parameters, we anticipate it could provide the experimental insights for nanopore fabrication by the laser-assisted dielectric breakdown method, enabling broader access to solid-state nanopores and their sensing applications.
Collapse
Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaodong He
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
22
|
Zhang Z, Wang X, Wei X, Zheng SW, Lenhart BJ, Xu P, Li J, Pan J, Albrecht H, Liu C. Multiplex quantitative detection of SARS-CoV-2 specific IgG and IgM antibodies based on DNA-assisted nanopore sensing. Biosens Bioelectron 2021; 181:113134. [PMID: 33761415 PMCID: PMC7927651 DOI: 10.1016/j.bios.2021.113134] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 02/06/2023]
Abstract
The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread into a global pandemic. Early and accurate diagnosis and quarantine remain the most effective mitigation strategy. Although reverse transcriptase polymerase chain reaction (RT-qPCR) is the gold standard for COVID-19 diagnosis, recent studies suggest that nucleic acids were undetectable in a significant number of cases with clinical features of COVID-19. Serologic assays that detect human antibodies to SARS-CoV-2 serve as a complementary method to diagnose these cases, as well as to identify asymptomatic cases and qualified convalescent serum donors. However, commercially available enzyme-linked immunosorbent assays (ELISA) are laborious and non-quantitative, while point-of-care assays suffer from low detection accuracy. To provide a serologic assay with high performance and portability for potential point-of-care applications, we developed DNA-assisted nanopore sensing for quantification of SARS-CoV-2 related antibodies in human serum. Different DNA structures were used as detection reporters for multiplex quantification of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against the nucleocapsid protein of SARS-CoV-2 in serum specimens from patients with conformed or suspected infection. Comparing to a clinically used point-of-care assay and an ELISA assay, our technology can reliably quantify SARS-CoV-2 antibodies with higher accuracy, large dynamic range, and potential for assay automation.
Collapse
Affiliation(s)
- Zehui Zhang
- Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaojun Wei
- Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA; Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA
| | - Sophia W Zheng
- Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA
| | - Brian J Lenhart
- Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA
| | - Peisheng Xu
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Jie Li
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Jing Pan
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Helmut Albrecht
- Department of Internal Medicine, School of Medicine, University of South Carolina, Columbia, SC 29209, USA; Department of Internal Medicine, Palmetto Health USC Medical Group, Columbia, SC 29203, USA
| | - Chang Liu
- Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA; Department of Chemical Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA.
| |
Collapse
|
23
|
Huang C, Zhu X, Li N, Ma X, Li Z, Fan J. Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level. J Phys Chem Lett 2021; 12:793-799. [PMID: 33411544 DOI: 10.1021/acs.jpclett.0c02989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The identification ability of nanopore sequencing is severely hindered by the diversity of amino acids in a protein. To tackle this problem, a graphene nanoslit sensor is adopted to collect force and current signals to distinguish 20 residues. Extensive molecular dynamics simulations are performed on sequencing peptides under pulling force and applied electric field. Results show that the signals of force and current can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between tyrosine and alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well-grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents. Generally, the graphene nanoslit sensor can be employed to simultaneously sense two signals, thereby enhancing the identification ability and providing an effective mode of nanopore protein sequencing.
Collapse
Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Na Li
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao, Shandong 266580, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| |
Collapse
|
24
|
Zhao D, Chen H, Wang Y, Li B, Duan C, Li Z, Li L. Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-020-2004-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
25
|
Lee SH, Rho WY, Chang H, Lee JH, Kim J, Lee SH, Jun BH. Carbon Nanomaterials for Biomedical Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1309:257-276. [PMID: 33782876 DOI: 10.1007/978-981-33-6158-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of carbon-based nanomaterials (CNs) with outstanding properties has been rising in many scientific and industrial application fields. These CNs represent a tunable alternative for applications with biomolecules, which allow interactions in either covalent or noncovalent way. Diverse carbon-derived nanomaterial family exhibits unique features and has been widely exploited in various biomedical applications, including biosensing, diagnosis, cancer therapy, drug delivery, and tissue engineering. In this chapter, we aim to present an overview of CNs with a particular interest in intrinsic structural, electronic, and chemical properties. In particular, the detailed properties and features of CNs and its derivatives, including carbon nanotube (CNT), graphene, graphene oxide (GO), and reduced GO (rGO) are summarized. The interesting biomedical applications are also reviewed in order to offer an overview of the possible fields for scientific and industrial applications of CNs.
Collapse
Affiliation(s)
- Sang Hun Lee
- Department of Chemical and Biological Engineering, Hanbat National University, Daejeon, Republic of Korea
| | - Won-Yeop Rho
- School of International Engineering and Science, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyejin Chang
- Division of Science Education, Kangwon National University, Chuncheon, Republic of Korea
| | - Jong Hun Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Republic of Korea
| | - Jaehi Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Seung Hwan Lee
- Department of Bionano Engineering, Hanyang University, Ansan, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
| |
Collapse
|
26
|
Jia X, Yang Y, Liu Y, Niu W, Li YQ, Zhao M, Mu Y, Li W. Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping. NANOSCALE ADVANCES 2020; 2:4539-4546. [PMID: 36132907 PMCID: PMC9417744 DOI: 10.1039/d0na00365d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/25/2020] [Indexed: 06/16/2023]
Abstract
In recent years, nanomaterials have attracted considerable research attention for biological and medical related applications due to their well-recognized physical and chemical properties. However, the deep understanding of the binding process at the protein-nanomaterial interface is essential to solve the concern of nano-toxicity. Here, we study the interactions between the recently reported graphenic nano-sheets, BC3 and C3N, and a prototypical protein (YAP65WW domain) via atomistic molecular dynamics simulations. Our simulations reveal that elemental doping is an effective way to tune the binding characteristics of YAP65WW with two nanomaterials. While YAP65WW can be attracted by two nanomaterials, the BC3 sheet is less able to disrupt the protein structure than C3N. From the energy point of view, this is because protein residues demonstrate a binding preference with the trend from electron rich nitrogen to electron deficient boron. Structural analyses of the bio-nano interface revealed the formation of an ordered water shell on the BC3 surface, which was compatible to the crystal pattern of BC3. When a protein binds with BC3, these interfacial water molecules protect the protein from being disrupted. We suggest that elemental doping is efficient to produce fruitful biological-effects of graphenic nanomaterials, which make it a prospective solution for the future design and fabrication of advanced nanomaterials with desired function.
Collapse
Affiliation(s)
- Xiao Jia
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yang Liu
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Weihua Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yong-Qiang Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Mingwen Zhao
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University 637551 Singapore
| | - Weifeng Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| |
Collapse
|
27
|
Wei X, Ma D, Jing L, Wang LY, Wang X, Zhang Z, Lenhart BJ, Yin Y, Wang Q, Liu C. Enabling nanopore technology for sensing individual amino acids by a derivatization strategy. J Mater Chem B 2020; 8:6792-6797. [PMID: 32495805 PMCID: PMC7429270 DOI: 10.1039/d0tb00895h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanopore technology holds remarkable promise for sequencing proteins and peptides. To achieve this, it is necessary to establish a characteristic profile for each individual amino acid through the statistical description of its translocation process. However, the subtle molecular differences among all twenty amino acids along with their unpredictable conformational changes at the nanopore sensing region result in very low distinguishability. Here we report the electrical sensing of individual amino acids using an α-hemolysin nanopore based on a derivatization strategy. Using derivatized amino acids as detection surrogates not only prolongs their interactions with the sensing region, but also improves their conformational variation. Furthermore, we show that distinct characteristics including current blockades and dwell times can be observed among all three classes of amino acids after 2,3-naphthalenedicarboxaldehyde (NDA)- and 2-naphthylisothiocyanate (NITC)-derivatization, respectively. These observable characteristics were applied towards the identification and differentiation of 9 of the 20 natural amino acids using their NITC derivatives. The method demonstrated herein will pave the way for the identification of all amino acids and further protein and peptide sequencing.
Collapse
Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Lihong Jing
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing 100190, China
| | - Leon Y. Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
| | - Brian J. Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
28
|
Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
Collapse
|
29
|
Wei X, Ma D, Zhang Z, Wang LY, Gray JL, Zhang L, Zhu T, Wang X, Lenhart BJ, Yin Y, Wang Q, Liu C. N-Terminal Derivatization-Assisted Identification of Individual Amino Acids Using a Biological Nanopore Sensor. ACS Sens 2020; 5:1707-1716. [PMID: 32403927 PMCID: PMC7978492 DOI: 10.1021/acssensors.0c00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nanopore technology has been employed as a powerful tool for DNA sequencing and analysis. To extend this method to peptide sequencing, a necessary step is to profile individual amino acids (AAs) through their nanopore stochastic signals, which remains a great challenge because of the low signal-to-noise ratio and unpredictable conformational changes of AAs during their translocation through nanopores. We showed that the combination of an N-terminal derivatization strategy of AAs with nanopore technology could lead to effective in situ differentiation of AAs. Four different derivatization reactions have been tested with five selected AAs: Ala, Phe, Tyr, His, and Asp. Using an α-hemolysin nanopore, we demonstrated the feasibility of derivatization-assisted identification of AAs regardless of their charge composition and polarity. The method was further applied to discriminate each individual AA in testing data sets using their established nanopore profiles from training data sets. We envision that this proof-of-concept study will not only pave a way for identification of individual AAs but also lead to future applications in protein/peptide sequencing using the nanopore technology.
Collapse
Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 Fujian, China
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Leon Y Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jonathan L Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Tianyu Zhu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Brian J Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 Fujian, China
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
30
|
Zhang Y, Zhou Y, Li Z, Chen H, Zhang L, Fan J. Computational investigation of geometrical effects in 2D boron nitride nanopores for DNA detection. NANOSCALE 2020; 12:10026-10034. [PMID: 32367083 DOI: 10.1039/c9nr10172a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopore-based DNA detection and analysis have been intensively pursued theoretically and experimentally over the past decade. Owing to their nanometer thickness, 2D nanopores, such as boron nitride nanopores, show great potential for achieving DNA detection at base resolution. Although 2D nanopore devices hold great promise for next-generation DNA detection, efficiently and reliably detecting different DNA sequences is still a challenging problem. To date, most of the investigated nanopores adopt circular shapes. Because of the successful fabrication of triangular nanopores, investigating the shape effect of nanopores for DNA detection has become more and more important. In this study, boron nitride nanopores with circular, hexagonal, quadrangular and triangular shapes were modeled at various sizes. The translocation of homogeneous dsDNA through these nanopores was investigated by all-atom molecular dynamic simulations. The ionic conductivity of these nanopores was characterized and formulas for the total resistance based on the pore and access resistance were derived. The ionic current, dwell time and conductance blockade of homogeneous dsDNA were compared for nanopores with different shapes. We demonstrate that the charge distribution at the pore mouth plays an important role in the transportation of ions and DNA molecules. Our findings may shed light on the design of 2D nanopores and can facilitate the development of fast, low-cost and reliable nanopore-based DNA detection.
Collapse
Affiliation(s)
- Yonghui Zhang
- School of Materials and Energy, Guangdong University of Technology, Guangzhou 510006, China.
| | | | | | | | | | | |
Collapse
|
31
|
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: 14] [Impact Index Per Article: 3.5] [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
|
32
|
Cecconi F, Chinappi M. Native-state fingerprint on the ubiquitin translocation across a nanopore. Phys Rev E 2020; 101:032401. [PMID: 32290013 DOI: 10.1103/physreve.101.032401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/11/2020] [Indexed: 11/07/2022]
Abstract
We study the translocation of the ubiquitin molecule (Ubq) across a channel with a double section which constitutes a general feature of several transmembrane nanopores such as the α-hemolysin (αHL). Our purpose is to establish the structure-dependent character of the Ubq translocation pathway. This implies to find the correspondence, if any, between the translocational unfolding steps and the Ubq native state. For this reason, it is convenient to apply a coarse-grained computational approach, where the protein is described only by the backbone and the force field only exploits the information contained in the native state (in the spirit of Gō-like models, or native-centric models). The αHL-like pore is portrayed as two coaxial confining cylinders: a larger one for the vestibule and a narrower one for the barrel (or stem). Such simplified approach allows a large number of translocation events to be collected by limited computational resources. The co-translocational unfolding of Ubq is described via a few collective variables that characterize the translocation progress. We find two translocation intermediates (stalled conformations) that can be associated with specific unfolding stages. In particular, in the earliest step, the strand S5 unfolds and enters the pore. This step splits the native conformation into two structural clusters packing against each other in the Ubq fold. A second stall occurs when the hairpin of the N terminal engages the stem region.
Collapse
Affiliation(s)
- Fabio Cecconi
- Istituto dei Sistemi Complessi (CNR), Via Taurini 19, I-00185 Roma, Italy
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Roma I-00133, Italy
| |
Collapse
|
33
|
Ouldali H, Sarthak K, Ensslen T, Piguet F, Manivet P, Pelta J, Behrends JC, Aksimentiev A, Oukhaled A. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat Biotechnol 2020; 38:176-181. [PMID: 31844293 PMCID: PMC7008938 DOI: 10.1038/s41587-019-0345-2] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 10/18/2019] [Accepted: 11/06/2019] [Indexed: 02/04/2023]
Abstract
Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.
Collapse
Affiliation(s)
- Hadjer Ouldali
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabien Piguet
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
- DreamPore S.A.S., 33 Boulevard du Port 95000, Cergy, France
| | - Philippe Manivet
- APHP, GHU APHP.Nord, DMU BioGem, Hôpital Lariboisière, BIOBANK Lariboisière Department BB-0033-00064, Plateforme de BioPathologie et de Technologies Innovantes en Santé, Paris, France
- INSERM UMR 1141 "NeuroDiderot", Université de Paris, Paris, France
| | - Juan Pelta
- LAMBE UMR 8587, Université d'Evry-Val-d'Essonne, CNRS, CEA, Université Paris-Saclay, Evry, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Freiburg Materials Research Centre (FMF), University of Freiburg, Freiburg, Germany
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Abdelghani Oukhaled
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France.
| |
Collapse
|
34
|
Liu F, Zhang Y, Wang H, Li L, Zhao W, Shen JW, Liang L. Study on the adsorption orientation of DNA on two-dimensional MoS2 surface via molecular dynamics simulation: A vertical orientation phenomenon. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110546] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
35
|
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: 164] [Impact Index Per Article: 41.0] [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
|
36
|
Lenhart B, Wei X, Zhang Z, Wang X, Wang Q, Liu C. Nanopore Fabrication and Application as Biosensors in Neurodegenerative Diseases. Crit Rev Biomed Eng 2020; 48:29-62. [PMID: 32749118 PMCID: PMC8020784 DOI: 10.1615/critrevbiomedeng.2020033151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since its conception as an applied biomedical technology nearly 30 years ago, nanopore is emerging as a promising, high-throughput, biomarker-targeted diagnostic tool for clinicians. The attraction of a nanopore-based detection system is its simple, inexpensive, robust, user-friendly, high-throughput blueprint with minimal sample preparation needed prior to analysis. The goal of clinical-based nanopore biosensing is to go from sample acquisition to a meaningful readout quickly. The most extensive work in nanopore applications has been targeted at DNA, RNA, and peptide identification. Although, biosensing of pathological biomarkers, which is covered in this review, is on the rise. This review is broken into two major sections: (i) the current state of existing biological, solid state, and hybrid nanopore systems and (ii) the applications of nanopore biosensors toward detecting neurodegenerative biomarkers.
Collapse
Affiliation(s)
- Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| |
Collapse
|
37
|
Gubbiotti A, Chinappi M, Casciola CM. Confinement effects on the dynamics of a rigid particle in a nanochannel. Phys Rev E 2019; 100:053307. [PMID: 31869915 DOI: 10.1103/physreve.100.053307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Indexed: 12/19/2022]
Abstract
The transport of nanoparticles in confined geometries plays a crucial role in several technological applications ranging from nanopore sensors to filtration membranes. Here we describe a Brownian approach to simulate the motion of a rigid-body nanoparticle of an arbitrary shape under confinement. A quaternion formulation is used for the nanoparticle orientation, and the corresponding overdamped Langevin equation, completed by the proper fluctuation-dissipation relation, is derived. The hydrodynamic mobility matrix is obtained via dissipative particle dynamics simulation equipped with a new method for enforcing the no-slip boundary condition for curved moving solid-liquid interfaces. As an application, we analyzed the motion of a nanoparticle in a cylindrical channel under the action of external fields. We show that both axial effective diffusion and rotational diffusion decrease with confinement.
Collapse
Affiliation(s)
- Alberto Gubbiotti
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Roma, Italia
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, 00133 Roma, Italia
| | - Carlo Massimo Casciola
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, 00184 Roma, Italia
| |
Collapse
|
38
|
Schwartz DC. Biophysics and the Genomic Sciences. Biophys J 2019; 117:2047-2053. [PMID: 31409480 DOI: 10.1016/j.bpj.2019.07.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/27/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
It is now rare to find biological, or genetic investigations that do not rely on the tools, data, and thinking drawn from the genomic sciences. Much of this revolution is powered by contemporary sequencing approaches that readily deliver large, genome-wide data sets that not only provide genetic insights but also uniquely report molecular outcomes from experiments that biophysicists are increasingly using for potentiating structural and mechanistic investigations. In this perspective, I describe a path of how biophysical thinking greatly contributed to this revolution in ways that parallel advancements in computer science through discussion of several key inventions, described as "foundational devices." These discussions also point at the future of how biophysics and the genomic sciences may become more finely integrated for empowering new measurement paradigms for biological investigations.
Collapse
Affiliation(s)
- David C Schwartz
- Department of Chemistry, Laboratory of Genetics, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison Wisconsin.
| |
Collapse
|
39
|
Tsutsui M, Yamazaki T, Tatematsu K, Yokota K, Esaki Y, Kubo Y, Deguchi H, Arima A, Kuroda S, Kawai T. High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore. NANOSCALE 2019; 11:20475-20484. [PMID: 31647092 DOI: 10.1039/c9nr07039g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si3N4 membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoko Yamazaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kenji Tatematsu
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan. and National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yuko Esaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Yukari Kubo
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Hiroko Deguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| |
Collapse
|
40
|
Zollo G, Rossini AE. Vibration assisted electron tunneling through nano-gaps in graphene nano-ribbons for amino-acid and peptide bond recognition. NANOSCALE ADVANCES 2019; 1:3547-3554. [PMID: 36133549 PMCID: PMC9417285 DOI: 10.1039/c9na00396g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 07/16/2019] [Indexed: 06/15/2023]
Abstract
Peptide bond and amino-acid recognition by tunneling current flowing across nano-gaps of graphene nano-ribbons has been recently discussed. Theoretical predictions of the tunneling current signals were used in the elastic regime showing peculiar fingerprints. However, inelastic scattering due to vibrations is expected to play an important role. Then, the proposed strategy for peptide sequencing and amino-acid recognition is revised in the light of such inelastic scattering phenomena. Phonon and local vibrational mode assisted current tunneling is calculated by treating electron-phonon scattering in the context of the lowest order expansion of the self-consistent Born approximation. We study Gly and Ala homo-peptides as an example of very similar, small and neutral amino-acids that would be indistinguishable by means of standard techniques, such as the ionic blockade current, in real peptides. We show that all the inelastic contributions to the tunneling current are in the bias range 0 V ≤ V ≤ 0.5 V and that they can be classified, from an atomistic point of view, in terms of energy sub-ranges that they belong to. Peculiar fingerprints can be found for the typical configurations that have been recently found for peptide bond recognition by tunneling current.
Collapse
Affiliation(s)
- Giuseppe Zollo
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria (Sezione di Fisica), Università di Roma "La Sapienza" Via A. Scarpa 14-16 00161 Rome Italy
| | - Aldo Eugenio Rossini
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria (Sezione di Fisica), Università di Roma "La Sapienza" Via A. Scarpa 14-16 00161 Rome Italy
| |
Collapse
|
41
|
Luo MB, Wu F, Zhang S, Sun LZ. Effect of temperature on the escape of charged polymer chain from a repulsive nanopore. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1629435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Meng-Bo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Fan Wu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Shuang Zhang
- College of Science, Beibu Gulf University, Qinzhou, People’s Republic of China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou, People’s Republic of China
| |
Collapse
|
42
|
Shankla M, Aksimentiev A. Step-defect guided delivery of DNA to a graphene nanopore. NATURE NANOTECHNOLOGY 2019; 14:858-865. [PMID: 31384038 PMCID: PMC6863603 DOI: 10.1038/s41565-019-0514-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 06/21/2019] [Indexed: 05/22/2023]
Abstract
Precision placement and transport of biomolecules are critical to many single-molecule manipulation and detection methods. One such method is nanopore sequencing, in which the delivery of biomolecules towards a nanopore controls the method's throughput. Using all-atom molecular dynamics, here we show that the precision transport of biomolecules can be realized by utilizing ubiquitous features of graphene surface-step defects that separate multilayer domains. Subject to an external force, we found that adsorbed DNA moved much faster down a step defect than up, and even faster along the defect edge, regardless of whether the motion was produced by a mechanical force or a solvent flow. We utilized this direction dependency to demonstrate a mechanical analogue of an electric diode and a system for delivering DNA molecules to a nanopore. The defect-guided delivery principle can be used for the separation, concentration and storage of scarce biomolecular species, on-demand chemical reactions and nanopore sensing.
Collapse
Affiliation(s)
- Manish Shankla
- Department of Physics, University of Illinois, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL, USA.
| |
Collapse
|
43
|
Girão AF, Serrano MC, Completo A, Marques PAAP. Do biomedical engineers dream of graphene sheets? Biomater Sci 2019; 7:1228-1239. [PMID: 30720810 DOI: 10.1039/c8bm01636d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the past few years, graphene has outstandingly emerged as a key nanomaterial for boosting the performance of commercial, industrial and scientific related technologies. The popularity of this novel nanomaterial in biomedical engineering is due to its excellent biological, electronic, optical and thermal properties that, as a whole, surpass the features of commonly used biomaterials and consequently open a wide range of applications so far within the reach of science fiction. In this minireview, the potential of graphene and its based materials in the expanding biomedical field is highlighted with focus on groundbreaking diagnostic, monitoring and therapeutic strategies. Some of the major challenges related to the synthesis and safety of graphene-based materials are also briefly discussed because of their critical importance in bringing this class of carbon materials closer to the clinic.
Collapse
Affiliation(s)
- André F Girão
- TEMA, Department of Mechanical Engineering, University of Aveiro (UA), 3810-193 Aveiro, Portugal.
| | | | | | | |
Collapse
|
44
|
Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations. Sci Rep 2019; 9:6440. [PMID: 31015503 PMCID: PMC6478933 DOI: 10.1038/s41598-019-42867-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.
Collapse
|
45
|
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: 22] [Impact Index Per Article: 4.4] [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
|
46
|
Tsutsui M, Yokota K, Nakada T, Arima A, Tonomura W, Taniguchi M, Washio T, Kawai T. Silicon substrate effects on ionic current blockade in solid-state nanopores. NANOSCALE 2019; 11:4190-4197. [PMID: 30793719 DOI: 10.1039/c8nr09042d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We investigated the roles of silicon substrate material compositions in ionic current blockade in solid-state nanopores. When detecting single nanoparticles using an ionic current in a Si3N4 nanopore supported on a doped silicon wafer, resistive pulses were found to be blunted significantly via signal retardation due to predominant contributions of large capacitance at the ultrathin membrane. Unexpectedly, in contrast, changing the substrate material to non-doped silicon led to the sharpening of the spike-like signal feature, suggesting a better temporal resolution of the cross-channel ionic current measurements by virtue of the thick intrinsic semiconductor layer that served to diminish the net chip capacitance. The present results suggest the importance of the choice of Si compositions regarding the capacitance effects to attain better spatiotemporal resolution in solid-state nanopore sensors.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Roshan KA, Tang Z, Guan W. High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore. NANOTECHNOLOGY 2019; 30:095502. [PMID: 30523901 DOI: 10.1088/1361-6528/aaf48e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigate the current transport characteristics in the electrolyte-dielectric-electrolyte structure commonly used in the in situ controlled breakdown (CBD) fabrication of solid-state nanopores. It is found that the stochastic breakdown process could lead to fidelity issues of false positives (an incorrect indication of a true nanopore formation) and false negatives (inability to detect initial nanopore formation). Robust and deterministic detection of initial physical breakdown to alleviate false positives and false negatives is critical for precise nanopore size control. To this end, we report a high fidelity moving Z-score method based CBD fabrication of solid-state nanopore. We demonstrate 100% success rate of realizing the initial nanopore conductance of 3 ± 1 nS (corresponds to size of 1.7 ± 0.6 nm) regardless of the dielectric membrane characteristics. Our study also elucidates the Joule heating is the dominant mechanism for electric field-based nanopore enlargement. Single DNA molecule sensing using nanopores fabricated by this method was successfully demonstrated. We anticipate the moving Z-score based CBD method could enable broader access to the solid state nanopore-based single molecule analysis.
Collapse
Affiliation(s)
- Kamyar Akbari Roshan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, United States of America
| | | | | |
Collapse
|
48
|
Sahu S, Zwolak M. Colloquium: Ionic phenomena in nanoscale pores through 2D materials. REVIEWS OF MODERN PHYSICS 2019; 91:10.1103/RevModPhys.91.021004. [PMID: 31579274 PMCID: PMC6774369 DOI: 10.1103/revmodphys.91.021004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS2), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and constrictions within these materials is a distinct realm of competing many-particle interactions (e.g., solvation/dehydration, electrostatic blockade, hydrogen bond dynamics) and confinement. This opens up alternative routes to creating biomimetic pores and may even give analogues of quantum phenomena, such as quantized conductance, in the classical domain. These prospects make membranes of 2D materials - i.e., 2D membranes - fascinating. We will discuss the physics and applications of ionic transport through nanopores in 2D membranes.
Collapse
Affiliation(s)
- Subin Sahu
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, USA
| | | |
Collapse
|
49
|
Wang ZW, Su D, Li XQ, Cao JJ, Yang DC, Liu JY. A H₂O₂-Responsive Boron Dipyrromethene-Based Photosensitizer for Imaging-Guided Photodynamic Therapy. Molecules 2018; 24:E32. [PMID: 30577688 PMCID: PMC6337283 DOI: 10.3390/molecules24010032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/23/2022] Open
Abstract
In this study, we demonstrate a novel H₂O₂ activatable photosensitizer (compound 7) which contains a diiodo distyryl boron dipyrromethene (BODIPY) core and an arylboronate group that quenches the excited state of the BODIPY dye by photoinduced electron transfer (PET). The BODIPY-based photosensitizer is highly soluble and remains nonaggregated in dimethyl sulfoxide (DMSO) as shown by the intense and sharp Q-band absorption (707 nm). As expected, compound 7 exhibits negligible fluorescence emission and singlet oxygen generation efficiency. However, upon interaction with H₂O₂, both the fluorescence emission and singlet oxygen production of the photosensitizer can be restored in phosphate buffered saline (PBS) solution and PBS buffer solution containing 20% DMSO as a result of the cleavage of the arylboronate group. Due to the higher concentration of H₂O₂ in cancer cells, compound 7 even with low concentration is particularly sensitive to human cervical carcinoma (HeLa) cells (IC50 = 0.95 μM) but hardly damage human embryonic lung fibroblast (HELF) cells. The results above suggest that this novel BODIPY derivative is a promising candidate for fluorescence imaging-guided photodynamic cancer therapy.
Collapse
Affiliation(s)
- Zhi-Wei Wang
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| | - Dan Su
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| | - Xiao-Qiang Li
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| | - Jing-Jing Cao
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| | - De-Chao Yang
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| | - Jian-Yong Liu
- State Key Laboratory of Photocatalysis on Energy and Environment & National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
| |
Collapse
|
50
|
Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat Biotechnol 2018; 36:nbt.4278. [PMID: 30346938 PMCID: PMC6482110 DOI: 10.1038/nbt.4278] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/21/2018] [Indexed: 11/09/2022]
Abstract
The identification and quantification of proteins lags behind DNA-sequencing methods in scale, sensitivity, and dynamic range. Here, we show that sparse amino acid-sequence information can be obtained for individual protein molecules for thousands to millions of molecules in parallel. We demonstrate selective fluorescence labeling of cysteine and lysine residues in peptide samples, immobilization of labeled peptides on a glass surface, and imaging by total internal reflection microscopy to monitor decreases in each molecule's fluorescence after consecutive rounds of Edman degradation. The obtained sparse fluorescent sequence of each molecule was then assigned to its parent protein in a reference database. We tested the method on synthetic and naturally derived peptide molecules in zeptomole-scale quantities. We also fluorescently labeled phosphoserines and achieved single-molecule positional readout of the phosphorylated sites. We measured >93% efficiencies for dye labeling, survival, and cleavage; further improvements should enable studies of increasingly complex proteomic mixtures, with the high sensitivity and digital quantification offered by single-molecule sequencing.
Collapse
Affiliation(s)
- Jagannath Swaminathan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Alexander A. Boulgakov
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Erik T. Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Angela M. Bardo
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - James L. Bachman
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Joseph Marotta
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Amber M. Johnson
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Eric V. Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| |
Collapse
|