1
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Liu W, Ma C, Wang H, Sha J. Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9622-9629. [PMID: 38652583 DOI: 10.1021/acs.langmuir.4c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas double-stranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Haiyan Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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2
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Mereuta L, Asandei A, Andricioaei I, Park J, Park Y, Luchian T. Considerable slowdown of short DNA fragment translocation across a protein nanopore using pH-induced generation of enthalpic traps inside the permeation pathway. NANOSCALE 2023; 15:14754-14763. [PMID: 37655668 DOI: 10.1039/d3nr03344a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
A pressing challenge in the realm of nanopore-based sensing technologies for nucleic acid characterization has been the cheap and efficient control of analyte translocation. To address this, a plethora of methods were tested, including mutagenesis, molecular motors, enzymes, or the optimization of experimental conditions. Herein, we present a paradigm exploiting the manipulation of electrostatic interactions between 22-mer single-stranded DNAs (22_ssDNA) and low pH-induced charges in the alpha-hemolysin (α-HL) nanopore, to efficiently control the passage of captured molecules. We discovered that in electrolytes buffered at pH = 5 and pH = 4.5 where the nanopore's vestibule and lumen become oppositely charged as compared to that at neutral pH, the electrostatic anchoring at these regions of a 22_ssDNA fragment leads to a dramatic increase of the translocation time, orders of magnitude larger compared to that at neutral pH. This pH-dependent tethering effect is reversible, side invariant, and sensitive to the ionic strength and ssDNA contour length. In the long run, our discovery has the potential to provide a simple read-out of the sequence of bases pertaining to short nucleotide sequences, thus extending the efficacy of current nanopore-based sequencers.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Ioan Andricioaei
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, CA 92617, USA
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania.
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3
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Afrasiabian N, Wei M, Denniston C. Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces. Biomacromolecules 2023; 24:4103-4112. [PMID: 37417981 PMCID: PMC10498446 DOI: 10.1021/acs.biomac.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.
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Affiliation(s)
- Navid Afrasiabian
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Matthew Wei
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Colin Denniston
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
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4
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Ozmaian M, Makarov DE. Long-lived metastable knots in polyampholyte chains. PLoS One 2023; 18:e0287200. [PMID: 37315055 PMCID: PMC10266668 DOI: 10.1371/journal.pone.0287200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
Knots in proteins and DNA are known to have significant effect on their equilibrium and dynamic properties as well as on their function. While knot dynamics and thermodynamics in electrically neutral and uniformly charged polymer chains are relatively well understood, proteins are generally polyampholytes, with varied charge distributions along their backbones. Here we use simulations of knotted polymer chains to show that variation in the charge distribution on a polyampholyte chain with zero net charge leads to significant variation in the resulting knot dynamics, with some charge distributions resulting in long-lived metastable knots that escape the (open-ended) chain on a timescale that is much longer than that for knots in electrically neutral chains. The knot dynamics in such systems can be described, quantitatively, using a simple one-dimensional model where the knot undergoes biased Brownian motion along a "reaction coordinate", equal to the knot size, in the presence of a potential of mean force. In this picture, long-lived knots result from charge sequences that create large electrostatic barriers to knot escape. This model allows us to predict knot lifetimes even when those times are not directly accessible by simulations.
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Affiliation(s)
- Masoumeh Ozmaian
- College of Engineering, West Texas A&M University, Canyon, Texas, United States of America
| | - Dmitrii E. Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States of America
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, United States of America
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5
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Șoldănescu I, Lobiuc A, Covașă M, Dimian M. Detection of Biological Molecules Using Nanopore Sensing Techniques. Biomedicines 2023; 11:1625. [PMID: 37371721 PMCID: PMC10295350 DOI: 10.3390/biomedicines11061625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.
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Affiliation(s)
- Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covașă
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
- Department of Computer, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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6
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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7
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Ge Y, Cui M, Zhang Q, Wang Y, Xi D. Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe. NANOSCALE ADVANCES 2022; 4:3883-3891. [PMID: 36133334 PMCID: PMC9470019 DOI: 10.1039/d2na00190j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Nanopore technology has attracted extensive attention due to its rapid, highly sensitive, and label-free performance. In this study, we aimed to identify proteinogenic amino acids using a wild-type aerolysin nanopore. Specifically, bipolar peptide probes were synthesised by linking four aspartic acid residues to the N-terminal and five arginine residues to the C-terminal of individual amino acids. With the help of the bipolar peptide carrier, 9 proteinogenic amino acids were reliably recognised based on current blockade and dwell time using an aerolysin nanopore. Furthermore, by changing the charge of the peptide probe, two of the five unrecognized amino acids above mentioned were identified. These findings promoted the application of aerolysin nanopores in proteinogenic amino acid recognition.
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Affiliation(s)
- Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Qiuqi Zhang
- The First School of Clinical Medicine, Southern Medical University Guangzhou 510515 P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
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8
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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.
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9
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Prajapati JD, Pangeni S, Aksoyoglu MA, Winterhalter M, Kleinekathöfer U. Changes in Salt Concentration Modify the Translocation of Neutral Molecules through a ΔCymA Nanopore in a Non-monotonic Manner. ACS NANO 2022; 16:7701-7712. [PMID: 35435659 DOI: 10.1021/acsnano.1c11471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The voltage-dependent transport through biological and artificial nanopores is being used in many applications such as DNA or protein sequencing and sensing. The primary approach to determine the transport has been to measure the temporal ion current fluctuations caused by solutes when applying external voltages. Crossing the nanoscale confinement in the presence of an applied electric field primarily relies on two factors, i.e., the electrophoretic drag and electroosmosis. The electroosmotic flow (EOF) is a voltage-dependent ion-associated flow of solvent molecules, i.e., usually water, and depends on many factors, such as pH, temperature, pore diameter, and also the concentration of ions. The exact interplay between these factors is so far poorly understood. In this joint experimental and computational study, we have investigated the dependence of the EOF on the concentration of the buffer salt by probing the transport of α-cyclodextrin molecules through the ΔCymA channel. For five different KCl concentrations in the range between 0.125 and 2 M, we performed applied-field molecular dynamics simulations and analyzed the ionic flow and the EOF across the ΔCymA pore. To our surprise, the concentration-dependent net ionic flux changes non-monotonically and nonlinearly and the EOF is seen to follow the same pattern. On the basis of these findings, we were able to correlate the concentration-dependent EOF with experimental kinetic constants for the translocation of α-cyclodextrin through the ΔCymA nanopore. Overall, the results further improve our understanding of the EOF-mediated transport through nanopores and show that the EOF needs to seriously be taken into consideration when analyzing the permeation of (neutral) substrates through nanopores.
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Affiliation(s)
| | - Sushil Pangeni
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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10
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Abstract
Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization-based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics.
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Affiliation(s)
- Brendan M Floyd
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
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11
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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.
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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.
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12
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Huo MZ, Hu ZL, Ying YL, Long YT. Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore. Proteomics 2021; 22:e2100041. [PMID: 34545670 DOI: 10.1002/pmic.202100041] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/08/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022]
Abstract
Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.
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Affiliation(s)
- Ming-Zhu Huo
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Zheng-Li Hu
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
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13
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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14
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Chen X, Chen J, Zhuo BY, Yang X, Luo MB. Simulation study for the pulling translocation of a polymer globule. Polym J 2021. [DOI: 10.1038/s41428-021-00502-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Wang J, Ying YL, Zhong CB, Zhang LM, Yan F, Long YT. Instrumentational implementation for parallelized nanopore electrochemical measurements. Analyst 2021; 146:4111-4120. [PMID: 34116564 DOI: 10.1039/d1an00471a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China. and Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Li-Min Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
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16
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021; 60:14738-14749. [DOI: 10.1002/anie.202013462] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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17
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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18
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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19
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Prajapati JD, Kleinekathöfer U. Voltage-Dependent Transport of Neutral Solutes through Nanopores: A Molecular View. J Phys Chem B 2020; 124:10718-10731. [PMID: 33175522 DOI: 10.1021/acs.jpcb.0c08401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The permeation of (neutral) molecules through nanopores in the presence of external voltages depends on several factors including pore electrostatics, electrophoretic force, and electro-osmotic drag. In earlier single-channel electrophysiology experiments, voltage-dependent asymmetric transport of neutral α-cyclodextrin (α-CD) molecules through the biological nanopore ΔCymA was observed. The voltage-dependent ion-associated flow of water, the so-called electro-osmotic flow, has been suggested to be the key factor behind the observed asymmetric behavior. The influence of pore electrostatics and electrophoretic force and their interplay with the electro-osmotic drag with varying buffers and voltages has not yet been analyzed at the molecular level. Hence, the detailed physical mechanism behind this intriguing permeation process is in part still unclear. In the present study, we have performed 36 μs all-atom free energy calculations by combining applied-field molecular dynamics simulations with metadynamics techniques. The influence of several ionic conditions as well as external voltages on the permeation of α-CD molecules across the ΔCymA pore has been investigated. To decipher the thermodynamic and kinetic details, the lowest energy paths and the permeation times for α-CD translocation have been estimated. In the presence of KCl or MgCl2 salts, the charge of the cations is found to control the direction and magnitude of the electro-osmotic flow, which in turn strongly affects α-CD permeation. Overall, the present findings significantly improve the fundamental understanding of the voltage-dependent transport of neutral solutes across nanopores.
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Affiliation(s)
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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20
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Lysenin Channels as Sensors for Ions and Molecules. SENSORS 2020; 20:s20216099. [PMID: 33120957 PMCID: PMC7663491 DOI: 10.3390/s20216099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Lysenin is a pore-forming protein extracted from the earthworm Eisenia fetida, which inserts large conductance pores in artificial and natural lipid membranes containing sphingomyelin. Its cytolytic and hemolytic activity is rather indicative of a pore-forming toxin; however, lysenin channels present intricate regulatory features manifested as a reduction in conductance upon exposure to multivalent ions. Lysenin pores also present a large unobstructed channel, which enables the translocation of analytes, such as short DNA and peptide molecules, driven by electrochemical gradients. These important features of lysenin channels provide opportunities for using them as sensors for a large variety of applications. In this respect, this literature review is focused on investigations aimed at the potential use of lysenin channels as analytical tools. The described explorations include interactions with multivalent inorganic and organic cations, analyses on the reversibility of such interactions, insights into the regulation mechanisms of lysenin channels, interactions with purines, stochastic sensing of peptides and DNA molecules, and evidence of molecular translocation. Lysenin channels present themselves as versatile sensing platforms that exploit either intrinsic regulatory features or the changes in ionic currents elicited when molecules thread the conducting pathway, which may be further developed into analytical tools of high specificity and sensitivity or exploited for other scientific biotechnological applications.
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21
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Wang S, Wang Y, Yan S, Du X, Zhang P, Chen HY, Huang S. Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux. ACS APPLIED MATERIALS & INTERFACES 2020; 12:26926-26935. [PMID: 32432849 DOI: 10.1021/acsami.0c05626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.
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Affiliation(s)
- Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
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22
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Hu F, Angelov B, Li S, Li N, Lin X, Zou A. Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore. Chembiochem 2020; 21:2467-2473. [DOI: 10.1002/cbic.202000119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/09/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Fangzhou Hu
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Borislav Angelov
- Institute of Physics, ELI BeamlinesAcademy of Sciences of the Czech Republic Na Slovance 2 18221 Prague Czech Republic
| | - Shuang Li
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Na Li
- National Center for Protein Science in ShanghaiZhangjiang LabShanghai Advanced Research Institute, CAS Shanghai 200120 P. R. China
| | - Xubo Lin
- Institute of Single Cell EngineeringBeijing Advanced Innovation Center for Biomedical EngineeringBeihang University Beijing 100191 P. R. China
| | - Aihua Zou
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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23
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Sun K, Ju Y, Chen C, Zhang P, Sawyer E, Luo Y, Geng J. Single‐Molecule Interaction of Peptides with a Biological Nanopore for Identification of Protease Activity. SMALL METHODS 2020. [DOI: 10.1002/smtd.201900892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Yuan Ju
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Chuan Chen
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Peng Zhang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Erica Sawyer
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
- Department of Biochemistry St. Lawrence University Canton NY 13617 USA
| | - Youfu Luo
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Jia Geng
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
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24
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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.
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25
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Ding T, Chen AK, Lu Z. The applications of nanopores in studies of proteins. Sci Bull (Beijing) 2019; 64:1456-1467. [PMID: 36659703 DOI: 10.1016/j.scib.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023]
Abstract
Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.
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Affiliation(s)
- Taoli Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Zuhong Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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26
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Willems K, Ruić D, Biesemans A, Galenkamp NS, Van Dorpe P, Maglia G. Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore. ACS NANO 2019; 13:9980-9992. [PMID: 31403770 PMCID: PMC6764111 DOI: 10.1021/acsnano.8b09137] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability to confine and to study single molecules has enabled important advances in natural and applied sciences. Recently, we have shown that unlabeled proteins can be confined inside the biological nanopore Cytolysin A (ClyA) and conformational changes monitored by ionic current recordings. However, trapping small proteins remains a challenge. Here, we describe a system where steric, electrostatic, electrophoretic, and electro-osmotic forces are exploited to immobilize a small protein, dihydrofolate reductase (DHFR), inside ClyA. Assisted by electrostatic simulations, we show that the dwell time of DHFR inside ClyA can be increased by orders of magnitude (from milliseconds to seconds) by manipulation of the DHFR charge distribution. Further, we describe a physical model that includes a double energy barrier and the main electrophoretic components for trapping DHFR inside the nanopore. Simultaneous fits to the voltage dependence of the dwell times allowed direct estimates of the cis and trans translocation probabilities, the mean dwell time, and the force exerted by the electro-osmotic flow on the protein (≅9 pN at -50 mV) to be retrieved. The observed binding of NADPH to the trapped DHFR molecules suggested that the engineered proteins remained folded and functional inside ClyA. Contact-free confinement of single proteins inside nanopores can be employed for the manipulation and localized delivery of individual proteins and will have further applications in single-molecule analyte sensing and enzymology studies.
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Affiliation(s)
- Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Dino Ruić
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Annemie Biesemans
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol Van Dorpe
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
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27
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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.
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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
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28
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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29
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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
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30
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Kwon JY, Kim MK, Mereuta L, Seo CH, Luchian T, Park Y. Mechanism of action of antimicrobial peptide P5 truncations against Pseudomonas aeruginosa and Staphylococcus aureus. AMB Express 2019; 9:122. [PMID: 31363941 PMCID: PMC6667604 DOI: 10.1186/s13568-019-0843-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/20/2019] [Indexed: 01/07/2023] Open
Abstract
Rates of microbial drug resistance are increasing worldwide; therefore, antimicrobial peptides (AMPs) are considered promising alternative therapeutic agents to antibiotics. AMPs are essential components of the innate immune system and exhibit broad-spectrum antimicrobial activity. P5 is a Cecropin A-Magainin 2 hybrid analog peptide with antimicrobial activity against Gram-negative and Gram-positive bacteria. In the present study, truncated peptides were designed to reduction length, retainment their antimicrobial activity and low toxicity at high concentrations compared with that of the parent peptide P5. The truncated peptides P5-CT1 and P5-NT1 exhibited antibacterial activities against both Gram-negative and Gram-positive bacteria. In contrast, P5-CT2, P5-CT3, P5-NT2, and P5-NT3 showed higher antibacterial activities against gram-positive bacteria compared to Gram-negative bacteria at low concentration of peptides. The truncated peptides showed lower hemolytic activity and toxic effects against mammalian cells compared with those of the parent peptide P5. The levels of several truncated peptides were maintained in the presence of physiological concentrations of salts, indicating their high stability. The results of flow cytometry, propidium iodide uptake, n-phenyl-1-naphthylamine uptake, and 3,3′-dipropylthiadicarbocyanine iodide assays showed that these truncated peptides killed microbial cells by increasing membrane permeability, thereby causing membrane damage. The results suggested that truncated peptides of P5 have good potential for use as novel antimicrobial agents.
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31
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Asandei A, Mereuta L, Park J, Seo CH, Park Y, Luchian T. Nonfunctionalized PNAs as Beacons for Nucleic Acid Detection in a Nanopore System. ACS Sens 2019; 4:1502-1507. [PMID: 31119934 DOI: 10.1021/acssensors.9b00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work, single-channel current recordings were used to selectively detect individual ssDNA strands in the vestibule of the α-hemolysin (α-HL) protein nanopore. The sensing mechanism was based on the detection of the intrinsic topological change of target ssDNA molecules after the hybridization with complementary PNA fragments. The readily distinguishable current signatures of PNA-DNA duplexes reversible association with the α-HL's vestibule, in terms of blockade amplitudes and kinetic features, allows specific detection of nucleic acid hybridization.
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Affiliation(s)
| | | | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, South Korea, 32588
| | - Chang Ho Seo
- Department of Bioinformatics, Kongju National University, Kongju, South Korea, 32588
| | - Yoonkyung Park
- Department of Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, South Korea, 61452
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32
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Mereuta L, Asandei A, Schiopu I, Park Y, Luchian T. Nanopore-Assisted, Sequence-Specific Detection, and Single-Molecule Hybridization Analysis of Short, Single-Stranded DNAs. Anal Chem 2019; 91:8630-8637. [PMID: 31194518 DOI: 10.1021/acs.analchem.9b02080] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report here on the ability of the α-hemolysin (α-HL) nanopore to achieve label-free, selective, and real-time detection of 15 nt long ssDNA fragments in solution, by exploiting their hybridization with freely added, polycationic peptides-functionalized PNAs. At the core of our work lies the paradigm that when PNAs and ssDNA are mixed together, the bulk concentration of free PNA decreases, depending upon the (mis)match degree between complementary strands and their relative concentrations. We demonstrate that the ssDNA sensing principle and throughput of the method are determined by the rate at which nonhybridized, polycationic peptides-functionalized PNA molecules arrive at the α-HL's vestibule entrance and thread into the nanopore. We found that with the application of a 30-fold salt gradient across the nanopore, the method enhances single-molecule detection sensitivity in the nanomolar range of ssDNA concentrations. This study demonstrates that the transmembrane potential-dependent unzip of single PNA-DNA duplexes at the α-HL's β-barrel entry permits discrimination between sequences that differ by one base pair.
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Affiliation(s)
| | | | | | - Yoonkyung Park
- Department of Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM) , Chosun University , Gwangju 61452 , Republic of Korea
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33
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Li Q, Ying YL, Liu SC, Lin Y, Long YT. Detection of Single Proteins with a General Nanopore Sensor. ACS Sens 2019; 4:1185-1189. [PMID: 30860364 DOI: 10.1021/acssensors.9b00228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single protein sensing based on solid-state nanopores is promising but challenging, because the fast translocation velocity of a protein is beyond the bandwidth of nanopore instruments. To decelerate the translocation speed, here, we employed a common protein cross-link interaction to achieve a general and robust nanopore sensing platform for single-molecule detection of protein. Benefiting from the EDC/NHS coupling interaction between nanopore and proteins, a 10-fold decrease in speed has been achieved. The clearly distinguishable current signatures further reveal that the anisotropic translocation of a protein, which are horizontal, vertical, and flipping transit inside nanopore confinement. This strategy provides a general platform for rapid detection of proteins as well as exploring fundamental protein dynamics at the single-molecule level.
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Affiliation(s)
- Qiao Li
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yao Lin
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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Ji Z, Guo P. Channel from bacterial virus T7 DNA packaging motor for the differentiation of peptides composed of a mixture of acidic and basic amino acids. Biomaterials 2019; 214:119222. [PMID: 31158604 DOI: 10.1016/j.biomaterials.2019.119222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/11/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
Abstract
Protein mutations can result in dysfunctional cell signaling pathways; therefore it is of significance to develop a robust platform for the detection of protein mutations. Here, we report that the channel of bacterial virus T7 DNA packaging motor is able to discriminate peptides containing a mixture of acidic (negatively charged) and basic (positively charged) amino acids. Peptides were differentiated based on their current signatures created by their unique charge compositions. In combination with protease digestion, peptides with the locational differences of single amino acid were also identified. The results suggest that the T7 motor channel has the potential for peptide differentiation, mutation verification, and analysis of protein sequence.
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Affiliation(s)
- Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center; The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center; The Ohio State University, Columbus, OH, USA.
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35
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Larimi MG, Mayse LA, Movileanu L. Interactions of a Polypeptide with a Protein Nanopore Under Crowding Conditions. ACS NANO 2019; 13:4469-4477. [PMID: 30925041 PMCID: PMC6482057 DOI: 10.1021/acsnano.9b00008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Molecular crowding, a ubiquitous feature of the cellular environment, has significant implications in the kinetics and equilibrium of biopolymer interactions. In this study, a single charged polypeptide is exposed to competing forces that drive it into a transmembrane protein pore versus forces that pull it outside. Using single-molecule electrophysiology, we provide compelling experimental evidence that the kinetic details of the polypeptide-pore interactions are substantially affected by high concentrations of less-penetrating polyethylene glycols (PEGs). At a polymer concentration above a critical value, the presence of these neutral macromolecular crowders increases the rate constant of association but decreases the rate constant of dissociation, resulting in a stronger polypeptide-pore interaction. Moreover, a larger-molecular weight PEG exhibits a lower rate constant of association but a higher rate constant of dissociation than those values corresponding to a smaller-molecular weight PEG. These outcomes are in accord with a lower diffusion constant of the polypeptide and higher depletion-attraction forces between the polypeptide and transmembrane protein pore under crowding and confinement conditions.
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Affiliation(s)
- Motahareh Ghahari Larimi
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Lauren Ashley Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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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.
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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
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Luchian T, Park Y, Asandei A, Schiopu I, Mereuta L, Apetrei A. Nanoscale Probing of Informational Polymers with Nanopores. Applications to Amyloidogenic Fragments, Peptides, and DNA-PNA Hybrids. Acc Chem Res 2019; 52:267-276. [PMID: 30605305 DOI: 10.1021/acs.accounts.8b00565] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decades long advances in nanotechnology, biomolecular sciences, and protein engineering ushered the introduction of groundbreaking technologies devoted to understanding how matter behaves at single particle level. Arguably, one of the simplest in concept is the nanopore-based paradigm, with deep roots in what is originally known as the Coulter counter, resistive-pulse technique. Historically, a nanopore system comprising the oligomeric protein generated by Staphylococcus aureus toxin α-hemolysin (α-HL) was first applied to detecting polynucleotides, as revealed in 1996 by John J. Kasianowicz, Eric Brandin, Daniel Branton, and David W. Deamer, in the Proceedings of the National Academy of Sciences. Nowadays, a wide variety of other solid-state or protein-based nanopores have emerged as efficient tools for stochastic sensing of analytes as small as single metal ions, handling single molecules, or real-time, label-free probing of chemical reactions at single-molecule level. In this Account, we demonstrate the usefulness of the α-HL nanopore on probing metal-induced folding of peptides, and to investigating the reversible binding of various metals to physiologically relevant amyloid fragments. The widely recognized Achilles heel of the approach, is the relatively short dwell time of the analytes inside the nanopore. This hinders the collection of sufficient data required to infer statistically meaningful conclusions about the physical or chemical state of the studied analyte. To mitigate this, various approaches were successfully applied in particular experiments, including but not restricted to altering physical parameters of the aqueous solution, downsizing the nanopore geometry, the controlled tuning of the balance between the electrostatic and electro-osmotic forces, coating nanopores with a fluid lipid bilayer, employing a pressure-voltage biased pore. From our perspective, in this Account, we will present two strategies aimed at controlling the analyte passage across the α-HL. First, we will reveal how the electroosmotic flow can be harnessed to control residence time, direction, and the sequence of spatiotemporal dynamics of a single peptide along the nanopore. This also allows one to identify the mesoscopic trajectory of a peptide exiting the nanopore through either the vestibule or β-barrel moiety. Second, we lay out the principles of an approach dubbed "nanopore tweezing", enabling simultaneous capture rate increase and escape rate decrease of a peptide from the α-HL, with the applied voltage. At its core, this method requires the creation of an electrical dipole on the peptide under study, via engineering positive and negative amino acid residues at the two ends of the peptide. Concise applications of this approach are being demonstrated, as in proof-of-concept experiments we probed the primary structure exploration of polypeptides, via discrimination between selected neutral amino acid residues. Another useful venue provided by the nanopores is represented by single-molecule force experiments on captured analytes inside the nanopore, which proved useful in exploring force-induced rupture of nucleic acids duplexes, hairpins, or various nucleic acids-ligand conjugates. We will show that when applied to oppositely charged, polypeptide-functionalized PNA-DNA duplexes, the nanopore tweezing introduces a new generation of force-spectroscopy nanopore-based platforms, facilitating unzipping of a captured duplex and enabling the duplex hybridization energy estimation.
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Affiliation(s)
- Tudor Luchian
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea 61452
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Irina Schiopu
- Interdisciplinary Research Institute, Sciences Department, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Loredana Mereuta
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Aurelia Apetrei
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
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Varongchayakul N, Song J, Meller A, Grinstaff MW. Single-molecule protein sensing in a nanopore: a tutorial. Chem Soc Rev 2018; 47:8512-8524. [PMID: 30328860 DOI: 10.1039/c8cs00106e] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteins are the structural elements and machinery of cells responsible for a functioning biological architecture and homeostasis. Advances in nanotechnology are catalyzing key breakthroughs in many areas, including the analysis and study of proteins at the single-molecule level. Nanopore sensing is at the forefront of this revolution. This tutorial review provides readers a guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores. Specifically, the review describes the key materials, nanoscale features, and design requirements of nanopores. It also discusses general design requirements as well as details on the analysis of protein translocation. Finally, the article provides the background necessary to understand current research trends and to encourage the identification of new biomedical applications for protein sensing using nanopores.
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Cressiot B, Greive SJ, Mojtabavi M, Antson AA, Wanunu M. Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors. Nat Commun 2018; 9:4652. [PMID: 30405123 PMCID: PMC6220183 DOI: 10.1038/s41467-018-07116-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopore-based sensors are advancing the sensitivity and selectivity of single-molecule detection in molecular medicine and biotechnology. Current electrical sensing devices are based on either membrane protein pores supported in planar lipid bilayers or solid-state (SS) pores fabricated in thin metallic membranes. While both types of nanosensors have been used in a variety of applications, each has inherent disadvantages that limit its use. Hybrid nanopores, consisting of a protein pore supported within a SS membrane, combine the robust nature of SS membranes with the precise and simple engineering of protein nanopores. We demonstrate here a novel lipid-free hybrid nanopore comprising a natural DNA pore from a thermostable virus, electrokinetically inserted into a larger nanopore supported in a silicon nitride membrane. The hybrid pore is stable and easy to fabricate, and, most importantly, exhibits low peripheral leakage allowing sensing and discrimination among different types of biomolecules.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.,LAMBE, Université d'Evry Val d'Essonne, Université de Cergy Pontoise, CNRS, CEA, Université Paris-Saclay, Evry, F-91025, France
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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41
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Mamad-Hemouch H, Bacri L, Huin C, Przybylski C, Thiébot B, Patriarche G, Jarroux N, Pelta J. Versatile cyclodextrin nanotube synthesis with functional anchors for efficient ion channel formation: design, characterization and ion conductance. NANOSCALE 2018; 10:15303-15316. [PMID: 30069556 DOI: 10.1039/c8nr02623h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biomimetic ion channels with different materials have been extensively designed to study the dynamics in a confined medium. These channels allow the development of several applications, such as ultra-fast sequencing and biomarker detection. When considering their synthesis, the use of cheap, non-cytotoxic and readily available materials is an increasing priority. Cyclodextrins, in supramolecular architectures, are widely utilized for pharmaceutical and biotechnological applications. Recent work has shown that short nanotubes (NTs) based on alpha-cyclodextrin (α-CD) assemble transient ion channels into membranes without cytotoxicity. In this study, we probe the influence of new cyclodextrin NT structural parameters and chemical modifications on channel formation, stability and electrical conductance. We report the successful synthesis of β- and γ-cyclodextrin nanotubes (β-CDNTs and γ-CDNTs), as evidenced by mass-spectrometry and high-resolution transmission electron microscopy. CDNTs were characterized by their length, diameter and number of CDs. Two hydrophobic groups, silylated or vinylated, were attached along the γ-CDNTs, improving the insertion time into the membrane. All NTs synthesized form spontaneous biomimetic ion channels. The hydrophobic NTs exhibit higher stability in membranes. Electrophysiological measurements show that ion transport is the main contribution of NT conductance and that the ion energy penalty for the entry into these NTs is similar to that of biological channels.
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Affiliation(s)
- Hajar Mamad-Hemouch
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.
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Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores. Polymers (Basel) 2018; 10:polym10080885. [PMID: 30960810 PMCID: PMC6403800 DOI: 10.3390/polym10080885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023] Open
Abstract
In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.
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Sarabadani J, Ala-Nissila T. Theory of pore-driven and end-pulled polymer translocation dynamics through a nanopore: an overview. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:274002. [PMID: 29794332 DOI: 10.1088/1361-648x/aac796] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We review recent progress on the theory of dynamics of polymer translocation through a nanopore based on the iso-flux tension propagation (IFTP) theory. We investigate both pore-driven translocation of flexible and a semi-flexible polymers, and the end-pulled case of flexible chains by means of the IFTP theory and extensive molecular dynamics (MD) simulations. The validity of the IFTP theory can be quantified by the waiting time distributions of the monomers which reveal the details of the dynamics of the translocation process. The IFTP theory allows a parameter-free description of the translocation process and can be used to derive exact analytic scaling forms in the appropriate limits, including the influence due to the pore friction that appears as a finite-size correction to asymptotic scaling. We show that in the case of pore-driven semi-flexible and end-pulled polymer chains the IFTP theory must be augmented with an explicit trans side friction term for a quantitative description of the translocation process.
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Affiliation(s)
- Jalal Sarabadani
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), 19395-5531, Tehran, Iran. Interdisciplinary Centre for Mathematical Modelling, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom. Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom. Department of Applied Physics and QTF Center of Excellence, Aalto University School of Science, PO Box 11000, FI-00076 Aalto, Espoo, Finland
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Ciuca A, Asandei A, Schiopu I, Apetrei A, Mereuta L, Seo CH, Park Y, Luchian T. Single-Molecule, Real-Time Dissecting of Peptide Nucleic Acid-DNA Duplexes with a Protein Nanopore Tweezer. Anal Chem 2018; 90:7682-7690. [PMID: 29799733 DOI: 10.1021/acs.analchem.8b01568] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptide nucleic acids (PNAs) are artificial, oligonucleotides analogues, where the sugar-phosphate backbone has been substituted with a peptide-like N-(2-aminoethyl)glycine backbone. Because of their inherent benefits, such as increased stability and enhanced binding affinity toward DNA or RNA substrates, PNAs are intensively studied and considered beneficial for the fields of materials and nanotechnology science. Herein, we designed cationic polypeptide-functionalized, 10-mer PNAs, and demonstrated the feasible detection of hybridization with short, complementary DNA substrates, following analytes interaction with the vestibule entry of an α-hemolysin (α-HL) nanopore. The opposite charged state at the polypeptide-functionalized PNA-DNA duplex extremities, facilitated unzipping of a captured duplex at the lumen entry of a voltage-biased nanopore, followed by monomers threading. These processes were resolvable and identifiable in real-time, from the temporal profile of the ionic current through a nanopore accompanying conformational changes of a single PNA-DNA duplex inside the α-HL nanopore. By employing a kinetic description within the discrete Markov chains theory, we proposed a minimalist kinetic model to successfully describe the electric force-induced strand separation in the duplex. The distinct interactions of the duplex at either end of the nanopore present powerful opportunities for introducing new generations of force-spectroscopy nanopore-based platforms, enabling from the same experiment duplex detection and assessment of interstrand base pairing energy.
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Affiliation(s)
- Andrei Ciuca
- Department of Physics , Alexandru I. Cuza University , Iasi 700506 , Romania
| | - Alina Asandei
- Interdisciplinary Research Department , Alexandru I. Cuza University , Iasi 700506 , Romania
| | - Irina Schiopu
- Interdisciplinary Research Department , Alexandru I. Cuza University , Iasi 700506 , Romania
| | - Aurelia Apetrei
- Department of Physics , Alexandru I. Cuza University , Iasi 700506 , Romania
| | - Loredana Mereuta
- Department of Physics , Alexandru I. Cuza University , Iasi 700506 , Romania
| | - Chang Ho Seo
- Department of Bioinformatics , Kongju National University , Kongju 32588 , South Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM) , Chosun University , Gwangju 61452 , South Korea
| | - Tudor Luchian
- Department of Physics , Alexandru I. Cuza University , Iasi 700506 , Romania
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ZHOU S, TANG P, WANG YJ, WANG L, WANG DQ. Applications of Nanopore Sensing in Detection of Toxic Molecules. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61089-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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46
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Chinappi M, Cecconi F. Protein sequencing via nanopore based devices: a nanofluidics perspective. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:204002. [PMID: 29595524 DOI: 10.1088/1361-648x/aababe] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteins perform a huge number of central functions in living organisms, thus all the new techniques allowing their precise, fast and accurate characterization at single-molecule level certainly represent a burst in proteomics with important biomedical impact. In this review, we describe the recent progresses in the developing of nanopore based devices for protein sequencing. We start with a critical analysis of the main technical requirements for nanopore protein sequencing, summarizing some ideas and methodologies that have recently appeared in the literature. In the last sections, we focus on the physical modelling of the transport phenomena occurring in nanopore based devices. The multiscale nature of the problem is discussed and, in this respect, some of the main possible computational approaches are illustrated.
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Affiliation(s)
- Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133 Roma, Italy
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47
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Li S, Cao C, Yang J, Long YT. Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore. ChemElectroChem 2018. [DOI: 10.1002/celc.201800288] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuang Li
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
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48
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Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore. Nat Commun 2018; 9:966. [PMID: 29511176 PMCID: PMC5840376 DOI: 10.1038/s41467-018-03418-2] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
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If Squeezed, a Camel Passes Through the Eye of a Needle: Voltage-Mediated Stretching of Dendrimers Facilitates Passage Through a Nanopore. J Membr Biol 2017; 251:405-417. [DOI: 10.1007/s00232-017-9999-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 10/30/2017] [Indexed: 12/31/2022]
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Wang Y, Tian K, Du X, Shi RC, Gu LQ. Remote Activation of a Nanopore for High-Performance Genetic Detection Using a pH Taxis-Mimicking Mechanism. Anal Chem 2017; 89:13039-13043. [PMID: 29183111 PMCID: PMC6174115 DOI: 10.1021/acs.analchem.7b03979] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerolysin protein pore has been widely used for sensing peptides and proteins. However, only a few groups explored this nanopore for nucleic acids detection. The challenge is the extremely low capture efficiency for nucleic acids (>10 bases), which severely lowers the sensitivity of an aerolysin-based genetic biosensor. Here we reported a simple and easy-to-operate approach to noncovalently transform aerolysin into a highly nucleic acids-sensitive nanopore. Through a remote pH-modulation mechanism, we simply lower the pH on one side of the pore, then aerolysin is immediately "activated" and enabled to capture target DNA/RNA efficiently from the opposite side of the pore. This mechanism also decelerates DNA translocation, a desired property for sequencing and gene detection, allowing temporal separation of DNAs in different lengths. This method provides insight into the nanopore engineering for biosensing, making aerolysin applicable in genetic and epigenetic detections of long nucleic acids.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiao Du
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Rui-Cheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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