1
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Mereuta L, Bhatti H, Asandei A, Cimpanu A, Ying YL, Long YT, Luchian T. Controlling DNA Fragments Translocation across Nanopores with the Synergic Use of Site-Directed Mutagenesis, pH-Dependent Charge Tuning, and Electroosmotic Flow. ACS APPLIED MATERIALS & INTERFACES 2024; 16:40100-40110. [PMID: 39038810 PMCID: PMC11299134 DOI: 10.1021/acsami.4c03848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024]
Abstract
Biological and solid-state nanopores are at the core of transformative techniques and nanodevices, democratizing the examination of matter and biochemical reactions at the single-molecule level, with low cost, portability, and simplicity in operation. One of the crucial hurdles in such endeavors is the fast analyte translocation, which limits characterization, and a rich number of strategies have been explored over the years to overcome this. Here, by site-directed mutagenesis on the α-hemolysin protein nanopore (α-HL), sought to replace selected amino acids with glycine, electrostatic binding sites were induced on the nanopore's vestibule and constriction region and achieved in the most favorable case a 20-fold increase in the translocation time of short single-stranded DNA (ssDNA) at neutral pH, with respect to the wild-type (WT) nanopore. We demonstrated an efficient tool of controlling the ssDNA translocation time, via the interplay between the nanopore-ssDNA surface electrostatic interactions and electroosmotic flow, all mediated by the pH-dependent ionization of amino acids lining the nanopore's translocation pathway. Our data also reveal the nonmonotonic, pH-induced alteration of ssDNA average translocation time. Unlike mildly acidic conditions (pH ∼ 4.7), at a pH ∼ 2.8 maintained symmetrically or asymmetrically across the WT α-HL, we evidenced the manifestation of a dominant electroosmotic flow, determining the speeding up of the ssDNA translocation across the nanopore by counteracting the ssDNA-nanopore attractive electrostatic interactions. We envision potential applications of the presented approach by enabling easy-to-use, real-time detection of short ssDNA sequences, without the need for complex biochemical modifications to the nanopore to mitigate the fast translocation of such sequences.
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Affiliation(s)
- Loredana Mereuta
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Huma Bhatti
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Alina Asandei
- Interdisciplinary
Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Adina Cimpanu
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Yi-Lun Ying
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- Molecular
Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Tudor Luchian
- Department
of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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2
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Ratinho L, Bacri L, Thiebot B, Cressiot B, Pelta J. Identification and Detection of a Peptide Biomarker and Its Enantiomer by Nanopore. ACS CENTRAL SCIENCE 2024; 10:1167-1178. [PMID: 38947203 PMCID: PMC11212137 DOI: 10.1021/acscentsci.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Until now, no fast, low-cost, and direct technique exists to identify and detect protein/peptide enantiomers, because their mass and charge are identical. They are essential since l- and d-protein enantiomers have different biological activities due to their unique conformations. Enantiomers have potential for diagnostic purposes for several diseases or normal bodily functions but have yet to be utilized. This work uses an aerolysin nanopore and electrical detection to identify vasopressin enantiomers, l-AVP and d-AVP, associated with different biological processes and pathologies. We show their identification according to their conformations, in either native or reducing conditions, using their specific electrical signature. To improve their identification, we used a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used the Monte Carlo prediction to assign each event type to a specific l- or d-AVP enantiomer.
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Affiliation(s)
- Laura Ratinho
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Laurent Bacri
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
| | - Bénédicte Thiebot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Benjamin Cressiot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Juan Pelta
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
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3
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Greive SJ, Bacri L, Cressiot B, Pelta J. Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning. ACS NANO 2024; 18:539-550. [PMID: 38134312 DOI: 10.1021/acsnano.3c08433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.
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Affiliation(s)
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
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4
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Tan F, Yan R, Zhao C, Zhao N. Translocation Dynamics of an Active Filament through a Long-Length Scale Channel. J Phys Chem B 2023; 127:8603-8615. [PMID: 37782905 DOI: 10.1021/acs.jpcb.3c04250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Active filament translocation through a confined space is crucial for diverse biological processes. By using Langevin dynamics simulations, we investigate the translocation dynamics of an axially self-propelled chain through a channel. First, results show a suggestive reciprocal scaling of translocation time versus active force. Second, in the case of a long channel, we demonstrate a very intriguing nonmonotonic change of translocation time with increasing channel width. The driving force shows a similar trend, providing a consistent picture to understand the unexpected channel width effect. In particular, in a moderately broad channel, the disordered chain conformation results in a loss of driving force and thus inhibits translocation dynamics. Chain adsorption might occur in a wide channel, which accounts for a facilitated translocation. Lastly, we connect the translocation process to tension propagation (TP). A modified TP picture is proposed to interpret the waiting time distribution. Our work highlights the new phenomenology owing to the crucial interplay of activity and spacial confinement, which drives the translocation dynamics, going beyond the traditional entropic barrier scenario.
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Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Chaonan Zhao
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610065, China
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5
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS NANO 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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6
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Li L, Wu J, Lyon CJ, Jiang L, Hu TY. Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications. BME FRONTIERS 2023; 4:0019. [PMID: 37849662 PMCID: PMC10521655 DOI: 10.34133/bmef.0019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/19/2023] [Indexed: 10/19/2023] Open
Abstract
Extensive effort has been devoted to the discovery, development, and validation of biomarkers for early disease diagnosis and prognosis as well as rapid evaluation of the response to therapeutic interventions. Genomic and transcriptomic profiling are well-established means to identify disease-associated biomarkers. However, analysis of disease-associated peptidomes can also identify novel peptide biomarkers or signatures that provide sensitive and specific diagnostic and prognostic information for specific malignant, chronic, and infectious diseases. Growing evidence also suggests that peptidomic changes in liquid biopsies may more effectively detect changes in disease pathophysiology than other molecular methods. Knowledge gained from peptide-based diagnostic, therapeutic, and imaging approaches has led to promising new theranostic applications that can increase their bioavailability in target tissues at reduced doses to decrease side effects and improve treatment responses. However, despite major advances, multiple factors can still affect the utility of peptidomic data. This review summarizes several remaining challenges that affect peptide biomarker discovery and their use as diagnostics, with a focus on technological advances that can improve the detection, identification, and monitoring of peptide biomarkers for personalized medicine.
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Affiliation(s)
- Lin Li
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Jing Wu
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Li Jiang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Tony Y. Hu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
- Department of Biomedical Engineering, School of Science and Engineering, Tulane University, New Orleans, LA, USA
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7
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Stierlen A, Greive SJ, Bacri L, Manivet P, Cressiot B, Pelta J. Nanopore Discrimination of Coagulation Biomarker Derivatives and Characterization of a Post-Translational Modification. ACS CENTRAL SCIENCE 2023; 9:228-238. [PMID: 36844502 PMCID: PMC9951287 DOI: 10.1021/acscentsci.2c01256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Indexed: 06/18/2023]
Abstract
One of the most important health challenges is the early and ongoing detection of disease for prevention, as well as personalized treatment management. Development of new sensitive analytical point-of-care tests are, therefore, necessary for direct biomarker detection from biofluids as critical tools to address the healthcare needs of an aging global population. Coagulation disorders associated with stroke, heart attack, or cancer are defined by an increased level of the fibrinopeptide A (FPA) biomarker, among others. This biomarker exists in more than one form: it can be post-translationally modified with a phosphate and also cleaved to form shorter peptides. Current assays are long and have difficulties in discriminating between these derivatives; hence, this is an underutilized biomarker for routine clinical practice. We use nanopore sensing to identify FPA, the phosphorylated FPA, and two derivatives. Each of these peptides is characterized by unique electrical signals for both dwell time and blockade level. We also show that the phosphorylated form of FPA can adopt two different conformations, each of which have different values for each electrical parameter. We were able to use these parameters to discriminate these peptides from a mix, thereby opening the way for the potential development of new point-of-care tests.
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Affiliation(s)
- Aïcha Stierlen
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
| | | | - Laurent Bacri
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Philippe Manivet
- Centre
de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75475 Paris, France
- Université
Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
| | | | - Juan Pelta
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
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9
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Mittal S, Manna S, Pathak B. Machine Learning Prediction of the Transmission Function for Protein Sequencing with Graphene Nanoslit. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51645-51655. [PMID: 36374991 DOI: 10.1021/acsami.2c13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein sequencing has rapidly changed the landscape of healthcare and life science by accelerating the growth of diagnostics and personalized medicines for a variety of fatal diseases. Next-generation nanopore/nanoslit sequencing is promising to achieve single-molecule resolution with chromosome-size-long readability. However, due to inherent complexity, high-throughput sequencing of all 20 amino acids demands different approaches. Aiming to accelerate the detection of amino acids, a general machine learning (ML) method has been developed for quick and accurate prediction of the transmission function for amino acid sequencing. Among the utilized ML models, the XGBoost regression model is found to be the most effective algorithm for fast prediction of the transmission function with a very low test root-mean-square error (RMSE ∼0.05). In addition, using the random forest ML classification technique, we are able to classify the neutral amino acids with a prediction accuracy of 100%. Therefore, our approach is an initiative for the prediction of the transmission function through ML and can provide a platform for the quick identification of amino acids with high accuracy.
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Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Souvik Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
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10
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Dynamics of DNA Through Solid‐state Nanopores Fabricated by Controlled Dielectric Breakdown. Chem Asian J 2022; 17:e202200888. [DOI: 10.1002/asia.202200888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/28/2022] [Indexed: 11/19/2022]
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11
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Aizawa M, Iwase H, Kamijo T, Yamaguchi A. Protein Condensation at Nanopore Entrances as Studied by Differential Scanning Calorimetry and Small-Angle Neutron Scattering. J Phys Chem Lett 2022; 13:8684-8691. [PMID: 36094403 DOI: 10.1021/acs.jpclett.2c01708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The condensation of globular myoglobin (Mb) at the pore entrances of mesoporous silica (MPS) with a series of pore diameters (4.2, 6.4, 7.7, and 9.0 nm) was examined by differential scanning calorimetry (DSC) and contrast-matching small-angle neutron scattering (CM-SANS) experiments. The DSC measurements were performed to estimate the amount of Mb adsorbed at two different adsorption sites, namely, the pore interior and the pore entrance regions. The CM-SANS measurements were conducted to observe condensation of Mb molecules at the pore entrance regions. Notably, the nanopore entrance with a diameter close to twice that of the Mb diameter was found to be the specific cavity to facilitate the condensation of globular Mb. The Mb condensation occurred at the entrances of the 6.4 nm pore during the adsorption uptake from concentrated Mb solutions, whereas the adsorption uptake from diluted Mb solutions induced the condensation of Mb at the entrances of the 7.7 nm pore.
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Affiliation(s)
- Mami Aizawa
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Hiroki Iwase
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki 319-1106, Japan
| | - Toshio Kamijo
- Department of Creative Engineering, National Institute of Technology, Tsuruoka College, 104 Sawada, Inooka, Tsuruoka, Yamagata 997-8511, Japan
| | - Akira Yamaguchi
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
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12
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Song Z, Liang Y, Yang J. Nanopore Detection Assisted DNA Information Processing. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12183135. [PMID: 36144924 PMCID: PMC9504103 DOI: 10.3390/nano12183135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 05/27/2023]
Abstract
The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.
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Affiliation(s)
- Zichen Song
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yuan Liang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
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13
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Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis. BIOSENSORS 2022; 12:bios12080596. [PMID: 36004992 PMCID: PMC9405897 DOI: 10.3390/bios12080596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022]
Abstract
Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore’s vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen–antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.
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14
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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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15
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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16
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Tang W, Fried JP, Tilley RD, Gooding JJ. Understanding and modelling the magnitude of the change in current of nanopore sensors. Chem Soc Rev 2022; 51:5757-5776. [PMID: 35748606 DOI: 10.1039/d1cs00972a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.
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Affiliation(s)
- Wenxian Tang
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jasper P Fried
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
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17
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Wang X, Stevens KC, Ting JM, Marras AE, Rezvan G, Wei X, Taheri-Qazvini N, Tirrell MV, Liu C. Translocation Behaviors of Synthetic Polyelectrolytes through Alpha-Hemolysin (α-HL) and Mycobacterium smegmatis Porin A (MspA) Nanopores. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2022; 169:057510. [PMID: 35599744 PMCID: PMC9121822 DOI: 10.1149/1945-7111/ac6c55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNAs have been used as probes for nanopore sensing of noncharged biomacromolecules due to its negative phosphate backbone. Inspired by this, we explored the potential of diblock synthetic polyelectrolytes as more flexible and inexpensive nanopore sensing probes by investigating translocation behaviors of PEO-b-PSS and PEO-b-PVBTMA through commonly used alpha-hemolysin (α-HL) and Mycobacterium smegmatis porin A (MspA) nanopores. Translocation recordings in different configurations of pore orientation and testing voltage indicated efficient PEO-b-PSS translocations through α-HL and PEO-b-PVBTMA translocations through MspA. This work provides insight into synthetic polyelectrolyte-based probes to expand probe selection and flexibility for nanopore sensing.
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Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kaden C. Stevens
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey M. Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander E. Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
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18
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Asandei A, Mereuta L, Bucataru IC, Park Y, Luchian T. A single-molecule insight into the ionic strength dependent, cationic peptide nucleic acids - oligonucleotides interactions. Chem Asian J 2022; 17:e202200261. [PMID: 35419929 DOI: 10.1002/asia.202200261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/12/2022] [Indexed: 11/08/2022]
Abstract
To alleviate solubility-related shortcomings associated with the use of neutral peptide nucleic acids (PNA), a powerful strategy is incorporate various charged sidechains onto the PNA structure. Here we employ a single-molecule technique and prove that the ionic current blockade signature of free poly(Arg)-PNAs and their corresponding duplexes with target ssDNAs interacting with a single a-hemolysin (a-HL) nanopore is highly ionic strength dependent, with high salt-containing electrolytes facilitating both capture and isolation of such complexes. Our data illustrate the effect of low ionic strength in reducing the effective volume of free poly(Arg)-PNAs and augmentation of their electrophoretic mobility while traversing the nanopore. We found that unlike in high salt electrolytes, the specific hybridization of cationic moiety-containing PNAs with complementary negatively charged ssDNAs in a salt concentration as low as 0.5 M is dramatically impeded. We suggest a scenario in which reduced charge screening by counterions in low salt electrolytes enables non-specific, electrostatic interactions with the anionic backbone of polynucleotides, thus reducing the ability of PNA-DNA complementary association via hydrogen bonding patterns. We applied an experimental strategy with spatially-separated poly(Arg)-PNAs and ssDNAs, and present evidence at the single-molecule level suggestive of the real-time, long-range interactions-driven formation of poly(Arg)-PNA-DNA complexes, as individual strands entering the nanopore from opposite directions collide inside a nanocavity.
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Affiliation(s)
- Alina Asandei
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, ICI, ROMANIA
| | - Loredana Mereuta
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, Physics, ROMANIA
| | - Ioana C Bucataru
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, Physics, ROMANIA
| | - Yoonkyung Park
- Chosun University, Department of Biomedical Science, ROMANIA
| | - Tudor Luchian
- Alexandru I. Cuza University, Physics, Blvd. Carol I, no. 11, 700506, Iasi, ROMANIA
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19
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Ying C, Houghtaling J, Mayer M. Effects of off-axis translocation through nanopores on the determination of shape and volume estimates for individual particles. NANOTECHNOLOGY 2022; 33:275501. [PMID: 35320779 DOI: 10.1088/1361-6528/ac6087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Resistive pulses generated by nanoparticles that translocate through a nanopore contain multi-parametric information about the physical properties of those particles. For example, non-spherical particles sample several different orientations during translocation, producing fluctuations in blockade current that relate to their shape. Due to the heterogenous distribution of electric field from the center to the wall of a nanopore while a particle travels through the pore, its radial position influences the blockade current, thereby affecting the quantification of parameters related to the particle's characteristics. Here, we investigate the influence of these off-axis effects on parameters estimated by performing finite element simulations of dielectric particles transiting a cylindrical nanopore. We varied the size, ellipsoidal shape, and radial position of individual particles, as well as the size of the nanopore. As expected, nanoparticles translocating near the nanopore wall produce increase current blockades, resulting in overestimates of particle volume. We demonstrated that off-axis effects also influence estimates of shape determined from resistive pulse analyses, sometimes producing a multiple-fold deviation in ellipsoidal length-to-diameter ratio between estimates and reference values. By using a nanopore with the minimum possible diameter that still allows the particle to rotate while translocating, off-axis effects on the determination of both volume and shape can be minimized. In addition, tethering the nanoparticles to a fluid coating on the nanopore wall makes it possible to determine an accurate particle shape with an overestimated volume. This work provides a framework to select optimal ratios of nanopore to nanoparticle size for experiments targeting free translocations.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Jared Houghtaling
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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20
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Review of the use of nanodevices to detect single molecules. Anal Biochem 2022; 654:114645. [DOI: 10.1016/j.ab.2022.114645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
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21
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Afshar Bakshloo M, Kasianowicz JJ, Pastoriza-Gallego M, Mathé J, Daniel R, Piguet F, Oukhaled A. Nanopore-Based Protein Identification. J Am Chem Soc 2022; 144:2716-2725. [PMID: 35120294 DOI: 10.1021/jacs.1c11758] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The implementation of a reliable, rapid, inexpensive, and simple method for whole-proteome identification would greatly benefit cell biology research and clinical medicine. Proteins are currently identified by cleaving them with proteases, detecting the polypeptide fragments with mass spectrometry, and mapping the latter to sequences in genomic/proteomic databases. Here, we demonstrate that the polypeptide fragments can instead be detected and classified at the single-molecule limit using a nanometer-scale pore formed by the protein aerolysin. Specifically, three different water-soluble proteins treated with the same protease, trypsin, produce different polypeptide fragments defined by the degree by which the latter reduce the nanopore's ionic current. The fragments identified with the aerolysin nanopore are consistent with the predicted fragments that trypsin could produce.
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Affiliation(s)
| | - John J Kasianowicz
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States.,Freiburg Institute for Advanced Studies, Universität Freiburg, 79104 Freiburg, Germany
| | | | - Jérôme Mathé
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, 91000, France
| | - Régis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, 91000, France
| | - Fabien Piguet
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, 95000, France
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22
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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23
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen H, Huang S. Allosteric Switching of Calmodulin in a
Mycobacterium smegmatis
porin A (MspA) Nanopore‐Trap. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Tiezheng Pan
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
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24
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen HY, Huang S. Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap. Angew Chem Int Ed Engl 2021; 60:23863-23870. [PMID: 34449124 DOI: 10.1002/anie.202110545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Indexed: 01/23/2023]
Abstract
Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca2+ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca2+ -free, Ca2+ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca2+ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg2+ /Sr2+ /Ba2+ /Ca2+ /Pb2+ /Tb3+ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Tiezheng Pan
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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25
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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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26
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Miyagi M, Takiguchi S, Hakamada K, Yohda M, Kawano R. Single polypeptide detection using a translocon EXP2 nanopore. Proteomics 2021; 22:e2100070. [PMID: 34411416 DOI: 10.1002/pmic.202100070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023]
Abstract
DNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites, and describe its pore-forming properties in the lipid bilayer. EXP2 mainly formed a nanopore with a diameter of 2.5 nm assembled from 7 monomers. Using the EXP2 nanopore allowed us to detect poly-L-lysine (PLL) at a single-molecule level. Furthermore, the EXP2 nanopore has sufficient resolution to distinguish the difference in molecular weight between two individual PLL, long PLL (Mw: 30,000-70,000) and short PLL (Mw: 10,000). Our results contribute to the accumulation of information for peptide-detectable nanopores.
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Affiliation(s)
- Mitsuki Miyagi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Kazuaki Hakamada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
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27
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Fennouri A, List J, Ducrey J, Dupasquier J, Sukyte V, Mayer SF, Vargas RD, Pascual Fernandez L, Bertani F, Rodriguez Gonzalo S, Yang J, Mayer M. Tuning the Diameter, Stability, and Membrane Affinity of Peptide Pores by DNA-Programmed Self-Assembly. ACS NANO 2021; 15:11263-11275. [PMID: 34128638 DOI: 10.1021/acsnano.0c10311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein pores recently enabled a breakthrough in bioanalytics by making it possible to sequence individual DNA and RNA strands during their translocation through the lumen of the pore. Despite this success and the overall promise of nanopore-based single-molecule analytics, protein pores have not yet reached their full potential for the analysis and characterization of globular biomolecules such as natively folded proteins. One reason is that the diameters of available protein pores are too small for accommodating the translocation of most folded globular proteins through their lumen. The work presented here provides a step toward overcoming this limitation by programmed self-assembly of α-helical pore-forming peptides with covalently attached single-stranded DNA (ssDNA). Specifically, hybridization of the peptide ceratotoxin A (CtxA) with N-terminally attached ssDNA to a complementary DNA template strand with 4, 8, or 12 hybridization sites made it possible to trigger the assembly of pores with various diameters ranging from approximately 0.5 to 4 nm. Hybridization of additional DNA strands to these assemblies achieved extended functionality in a modular fashion without the need for modifying the amino acid sequence of the peptides. For instance, functionalization of these semisynthetic biological nanopores with DNA-cholesterol anchors increased their affinity to lipid membranes compared to pores formed by native CtxA, while charged transmembrane segments prolonged their open-state lifetime. Assembly of these hybrid DNA-peptides by a template increased their cytotoxic activity and made it possible to kill cancer cells at 20-fold lower total peptide concentrations than nontemplated CtxA.
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Affiliation(s)
- Aziz Fennouri
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Julie Ducrey
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jessica Dupasquier
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Viktorija Sukyte
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Simon F Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Reyner D Vargas
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Laura Pascual Fernandez
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Frederick Bertani
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Sandra Rodriguez Gonzalo
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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28
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Goto-Silva L, Junqueira M. Single-cell proteomics: A treasure trove in neurobiology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140658. [PMID: 33845200 DOI: 10.1016/j.bbapap.2021.140658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022]
Abstract
Single-cell analysis came to change the way we look at cell populations. RNA sequencing of single cells allowed us to appreciate the diversity of cell types in the human brain in an unprecedented manner and its power to reveal cell-type specific changes in cell populations has just begun to be explored. In this context, looking at the proteome of single cells promises to bring functional information and contribute to completing the picture. The potential of single cell proteome, in developing a better understanding of the intricate connections between the very diverse cell populations in the brain, is huge. Whereas early approaches to address single-cell proteome have identified hundreds of proteins, today, techniques combining isobaric labelling and LC-MS can lead to the identification of thousands of proteins. In this review, we describe methods which have been used to identify and quantify proteins from single cells and propose that the application of isobaric labeling and label-free quantitative proteomics approach for single-cell analysis is ready to provide useful information for the neurobiology field.
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Affiliation(s)
- Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), 22281-100 Rio de Janeiro, Brazil
| | - Magno Junqueira
- Proteomics Unit, Department of Biochemistry, Chemistry Institute, Federal University of Rio de janeiro, 21941-909 Rio de Janeiro, Brazil.
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Wei X, Zhang Z, Wang X, Lenhart B, Gambarini R, Gray J, Liu C. Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore. NANOTECHNOLOGY AND PRECISION ENGINEERING 2021; 3:2-8. [PMID: 33786424 PMCID: PMC8006565 DOI: 10.1016/j.npe.2019.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various molecules. However, the effect of several electrochemical factors on the host-guest interactions in nanopore still remains unknown. Here, we systematically studied host-guest interactions, especially oscillation of DNA-azide adamantane@cucurbit[6] in α-Hemolysin nanopore under varying pH, concentration of electrolytes and counterions (Li+, Na+, K+). Our results indicate correlations between the change of pH and the duration of the oscillation signal. In addition, the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals, and even the integrity of the protein nanopore. This study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Roberto Gambarini
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jonathan Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
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Nivala J, Mulroney L, Luan Q, Abu-Shumays R, Akeson M. Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP. Methods Mol Biol 2021; 2186:145-155. [PMID: 32918735 DOI: 10.1007/978-1-0716-0806-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins present a significant challenge for nanopore-based sequence analysis. This is partly due to their stable tertiary structures that must be unfolded for linear translocation, and the absence of regular charge density. To address these challenges, here we describe how ClpXP, an ATP-dependent protein unfoldase, can be harnessed to unfold and processively translocate multi-domain protein substrates through an alpha-hemolysin nanopore sensor. This process results in ionic current patterns that are diagnostic of protein sequence and structure at the single-molecule level.
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Affiliation(s)
- Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Logan Mulroney
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Qing Luan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Robin Abu-Shumays
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
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31
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Haji Abdolvahab R, Niknam Hamidabad M. Pore shapes effects on polymer translocation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:76. [PMID: 33306147 DOI: 10.1140/epje/i2020-12001-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.
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32
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Li MY, Ying YL, Li S, Wang YQ, Wu XY, Long YT. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore. ACS NANO 2020; 14:12571-12578. [PMID: 32806044 DOI: 10.1021/acsnano.0c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 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, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Xue-Yuan Wu
- 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
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Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
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Mereuta L, Asandei A, Dragomir IS, Bucataru IC, Park J, Seo CH, Park Y, Luchian T. Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach. Sci Rep 2020; 10:11323. [PMID: 32647249 PMCID: PMC7347621 DOI: 10.1038/s41598-020-68258-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania.
| | - Alina Asandei
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Isabela S Dragomir
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Ioana C Bucataru
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Chang Ho Seo
- 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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Hagan JT, Sheetz BS, Bandara YMNDY, Karawdeniya BI, Morris MA, Chevalier RB, Dwyer JR. Chemically tailoring nanopores for single-molecule sensing and glycomics. Anal Bioanal Chem 2020; 412:6639-6654. [PMID: 32488384 DOI: 10.1007/s00216-020-02717-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Brian S Sheetz
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Buddini I Karawdeniya
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Melissa A Morris
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Robert B Chevalier
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA.
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36
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Huang G, Willems K, Bartelds M, van Dorpe P, Soskine M, Maglia G. Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores. NANO LETTERS 2020; 20:3819-3827. [PMID: 32271587 PMCID: PMC7227020 DOI: 10.1021/acs.nanolett.0c00877] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Indexed: 05/19/2023]
Abstract
Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.
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Affiliation(s)
- Gang Huang
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
- imec, Kapeldreef 75, 3001 Leuven, Belgium
| | - Mart Bartelds
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol van Dorpe
- imec, Kapeldreef 75, 3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Misha Soskine
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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37
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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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Ramírez-Carreto S, Miranda-Zaragoza B, Rodríguez-Almazán C. Actinoporins: From the Structure and Function to the Generation of Biotechnological and Therapeutic Tools. Biomolecules 2020; 10:E539. [PMID: 32252469 PMCID: PMC7226409 DOI: 10.3390/biom10040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022] Open
Abstract
Actinoporins (APs) are a family of pore-forming toxins (PFTs) from sea anemones. These biomolecules exhibit the ability to exist as soluble monomers within an aqueous medium or as constitutively open oligomers in biological membranes. Through their conformational plasticity, actinoporins are considered good candidate molecules to be included for the rational design of molecular tools, such as immunotoxins directed against tumor cells and stochastic biosensors based on nanopores to analyze unique DNA or protein molecules. Additionally, the ability of these proteins to bind to sphingomyelin (SM) facilitates their use for the design of molecular probes to identify SM in the cells. The immunomodulatory activity of actinoporins in liposomal formulations for vaccine development has also been evaluated. In this review, we describe the potential of actinoporins for use in the development of molecular tools that could be used for possible medical and biotechnological applications.
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Affiliation(s)
| | | | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico; (S.R.-C.); (B.M.-Z.)
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Wan Y, Zhao J, He J, Lou X. Nano-Affi: a solution-phase, label-free, colorimetric aptamer affinity assay based on binding-inhibited aggregation of gold nanoparticles. Analyst 2020; 145:4276-4282. [DOI: 10.1039/d0an00827c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ideal way to assess aptamer affinity is when both aptamer and target are in a native state, without the unpredictable interference associated with labelling and surface immobilization.
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Affiliation(s)
- Yuan Wan
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Jiaxing Zhao
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing
- China
| | - Xinhui Lou
- Department of Chemistry
- Capital Normal University
- Beijing
- China
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40
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Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
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41
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Wu X, Li M, Ying Y, Long Y. The Effects of Tetramethylammonium Cation on Oligonucleotide Analysis with Aerolysin Nanopore. ChemElectroChem 2019. [DOI: 10.1002/celc.201901376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xue‐Yuan Wu
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Meng‐Yin Li
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi‐Lun Ying
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
| | - Yi‐Tao Long
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
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42
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43
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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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Protein fingerprinting with digital sequences of linear protein subsequence volumes: a computational study. J Biosci 2019. [DOI: 10.1007/s12038-019-9863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations. Sci Rep 2019; 9:6440. [PMID: 31015503 PMCID: PMC6478933 DOI: 10.1038/s41598-019-42867-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.
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Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
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Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
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48
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Wells CC, Melnikov DV, Gracheva ME. Brownian dynamics of a neutral protein moving through a nanopore in an electrically biased membrane. J Chem Phys 2019; 150:115103. [DOI: 10.1063/1.5080944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Craig C. Wells
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
| | | | - Maria E. Gracheva
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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50
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Sui XJ, Li MY, Ying YL, Yan BY, Wang HF, Zhou JL, Gu Z, Long YT. Aerolysin Nanopore Identification of Single Nucleotides Using the AdaBoost Model. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00088-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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