1
|
Namani S, Kavetsky K, Lin CY, Maharjan S, Gamper HB, Li NS, Piccirilli JA, Hou YM, Drndic M. Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores. ACS NANO 2024; 18:17240-17250. [PMID: 38906834 DOI: 10.1021/acsnano.4c04625] [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: 06/23/2024]
Abstract
This study investigates transfer ribonucleic acid (tRNA) conformational dynamics in the context of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) using solid-state silicon nitride (SiN) nanopore technology. SiN nanopores in thin membranes with specific dimensions exhibit high signal resolution, enabling real-time and single-molecule electronic detection of tRNA conformational changes. We focus on human mitochondrial tRNALeu(UAA) (mt-Leu(UAA)) that decodes Leu codons UUA/UUG (UUR) during protein synthesis on the mt-ribosome. The single A14G substitution in mt-Leu(UAA) is the major cause of MELAS disease. Measurements of current blockades and dwell times reveal distinct conformational dynamics of the wild-type (WT) and the A14G variant of mt-Leu(UAA) in response to the conserved post-transcriptional m1G9 methylation. While the m1G9-modified WT transcript adopts a more stable structure relative to the unmodified transcript, the m1G9-modified MELAS transcript adopts a less stable structure relative to the unmodified transcript. Notably, these differential features were observed at 0.4 M KCl, but not at 3 M KCl, highlighting the importance of experimental settings that are closer to physiological conditions. This work demonstrates the feasibility of the nanopore platform to discern tRNA molecules that differ by a single-nucleotide substitution or by a single methylation event, providing an important step forward to explore changes in the conformational dynamics of other RNA molecules in human diseases.
Collapse
Affiliation(s)
- Srilahari Namani
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyril Kavetsky
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Marija Drndic
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
2
|
de Blois C, Engel M, Rejou MA, Molcrette B, Favier A, Montel F. Optical single molecule characterisation of natural and synthetic polymers through nanopores. NANOSCALE 2023; 16:138-151. [PMID: 38054974 DOI: 10.1039/d3nr04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Nanopore techniques are now widely used to sequence DNA, RNA and even oligopeptide molecules at the base pair level by measuring the ionic current. In order to build a more versatile characterisation system, optical methods for the detection of a single molecule translocating through a nanopore have been developed, achieving very promising results. In this work, we developed a series of tools to interpret the optical signals in terms of the physical behaviour of various types of natural and synthetic polymers, with high throughput. We show that the measurement of the characteristic time of a translocation event gives access to the apparent molecular weight of an object, and allows us to quantify the concentration ratio of two DNA samples of different molecular weights in solution. Using the same tools for smaller synthetic polymers, we were able to obtain information about their molecular weight distribution depending on the synthesis method.
Collapse
Affiliation(s)
- Charlotte de Blois
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie Engel
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie-Amélie Rejou
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Bastien Molcrette
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Arnaud Favier
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Fabien Montel
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| |
Collapse
|
3
|
Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
Collapse
Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| |
Collapse
|
4
|
Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
Collapse
Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| |
Collapse
|
5
|
Yu L, Chen B, Li Z, Huang Q, He K, Su Y, Han Z, Zhou Y, Zhu X, Yan D, Dong R. Digital synthetic polymers for information storage. Chem Soc Rev 2023; 52:1529-1548. [PMID: 36786068 DOI: 10.1039/d2cs01022d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Digital synthetic polymers with uniform chain lengths and defined monomer sequences have recently become intriguing alternatives to traditional silicon-based information devices or natural biomacromolecules for data storage. The structural diversity of information-containing macromolecules endows the digital synthetic polymers with higher stability and storage density but less occupied space. Through subtly designing each unit of coded structure, the information can be readily encoded into digital synthetic polymers in a more economical scheme and more decodable, opening up new avenues for molecular digital data storage with high-level security. This tutorial review summarizes recent advances in salient features of digital synthetic polymers for data storage, including encoding, decoding, editing, erasing, encrypting, and repairing. The current challenges and outlook are finally discussed to offer potential solution guidance and new perspectives for the creation of next-generation digital synthetic polymers and broaden the scope of their applicability.
Collapse
Affiliation(s)
- Li Yu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Baiyang Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Ziying Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Qijing Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Kaiyuan He
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Yue Su
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Yongfeng Zhou
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Ruijiao Dong
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| |
Collapse
|
6
|
Bayat P, Rambaud C, Priem B, Bourderioux M, Bilong M, Poyer S, Pastoriza-Gallego M, Oukhaled A, Mathé J, Daniel R. Comprehensive structural assignment of glycosaminoglycan oligo- and polysaccharides by protein nanopore. Nat Commun 2022; 13:5113. [PMID: 36042212 PMCID: PMC9427770 DOI: 10.1038/s41467-022-32800-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
Glycosaminoglycans are highly anionic functional polysaccharides with information content in their structure that plays a major role in the communication between the cell and the extracellular environment. The study presented here reports the label-free detection and analysis of glycosaminoglycan molecules at the single molecule level using sensing by biological nanopore, thus addressing the need to decipher structural information in oligo- and polysaccharide sequences, which remains a major challenge for glycoscience. We demonstrate that a wild-type aerolysin nanopore can detect and characterize glycosaminoglycan oligosaccharides with various sulfate patterns, osidic bonds and epimers of uronic acid residues. Size discrimination of tetra- to icosasaccharides from heparin, chondroitin sulfate and dermatan sulfate was investigated and we show that different contents and distributions of sulfate groups can be detected. Remarkably, differences in α/β anomerization and 1,4/1,3 osidic linkages can also be detected in heparosan and hyaluronic acid, as well as the subtle difference between the glucuronic/iduronic epimers in chondroitin and dermatan sulfate. Although, at this stage, discrimination of each of the constituent units of GAGs is not yet achieved at the single-molecule level, the resolution reached in this study is an essential step toward this ultimate goal.
Collapse
Affiliation(s)
- Parisa Bayat
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Charlotte Rambaud
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Bernard Priem
- CNRS, CERMAV, University Grenoble Alpes, Grenoble, France
| | | | - Mélanie Bilong
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Salomé Poyer
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | | | | | - Jérôme Mathé
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
| | - Régis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
| |
Collapse
|
7
|
Ensslen T, Sarthak K, Aksimentiev A, Behrends JC. Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape. J Am Chem Soc 2022; 144:16060-16068. [PMID: 36007197 DOI: 10.1021/jacs.2c06211] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chemical nature and precise position of posttranslational modifications (PTMs) in proteins or peptides are crucial for various severe diseases, such as cancer. State-of-the-art PTM diagnosis is based on elaborate and costly mass-spectrometry or immunoassay-based approaches, which are limited in selectivity and specificity. Here, we demonstrate the use of a protein nanopore to differentiate peptides─derived from human histone H4 protein─of identical mass according to the positions of acetylated and methylated lysine residues. Unlike sequencing by stepwise threading, our method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, thus eliminating the need for controlled translocation. Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. This molecular shape-sensing principle offers a path to versatile, label-free, and high-throughput characterizations of protein isoforms.
Collapse
Affiliation(s)
- Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Kumar Sarthak
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
8
|
Versloot RA, Lucas FL, Yakovlieva L, Tadema MJ, Zhang Y, Wood TM, Martin NI, Marrink SJ, Walvoort MTC, Maglia G. Quantification of Protein Glycosylation Using Nanopores. NANO LETTERS 2022; 22:5357-5364. [PMID: 35766994 PMCID: PMC9284675 DOI: 10.1021/acs.nanolett.2c01338] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Although nanopores can be used for single-molecule sequencing of nucleic acids using low-cost portable devices, the characterization of proteins and their modifications has yet to be established. Here, we show that hydrophilic or glycosylated peptides translocate too quickly across FraC nanopores to be recognized. However, high ionic strengths (i.e., 3 M LiCl) and low pH (i.e., pH 3) together with using a nanopore with a phenylalanine at its constriction allows the recognition of hydrophilic peptides, and to distinguish between mono- and diglycosylated peptides. Using these conditions, we devise a nanopore method to detect, characterize, and quantify post-translational modifications in generic proteins, which is one of the pressing challenges in proteomic analysis.
Collapse
Affiliation(s)
| | | | - Liubov Yakovlieva
- Chemical
Biology Division, Stratingh Institute for Chemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | - Matthijs Jonathan Tadema
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Yurui Zhang
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Thomas M. Wood
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Chemical
Biology Division, Stratingh Institute for Chemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| |
Collapse
|
9
|
Han WB, Kang DH, Kim TS. 3D Artificial Cell Membranes as Versatile Platforms for Biological Applications. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Wei W, Chen X, Wang X. Nanopore Sensing Technique for Studying the Hofmeister Effect. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200921. [PMID: 35484475 DOI: 10.1002/smll.202200921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The nanopore sensing technique is an emerging method of detecting single molecules, and extensive research has gone into various fields, including nanopore sequencing and other applications of single-molecule studies. Recently, several researchers have explored the specific ion effects in nanopore channels, enabling a unique understanding of the Hofmeister effect at the single-molecule level. Herein, the recent advances of using nanopore sensing techniques are reviewed to study the Hofmeister effect and the physicochemical mechanism of this process is attempted. The challenges and goals are also discussed for the future in this field.
Collapse
Affiliation(s)
- Weichen Wei
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xiaojuan Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xuejiao Wang
- Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, China
| |
Collapse
|
11
|
Versloot RA, Straathof SA, Stouwie G, Tadema MJ, Maglia G. β-Barrel Nanopores with an Acidic-Aromatic Sensing Region Identify Proteinogenic Peptides at Low pH. ACS NANO 2022; 16:7258-7268. [PMID: 35302739 PMCID: PMC9134492 DOI: 10.1021/acsnano.1c11455] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Biological nanopores are emerging as sensitive single-molecule sensors for proteins and peptides. The heterogeneous charge of a polypeptide chain, however, can complicate or prevent the capture and translocation of peptides and unfolded proteins across nanopores. Here, we show that two β-barrel nanopores, aerolysin and cytotoxin K, cannot efficiently detect proteinogenic peptides from a trypsinated protein under a wide range of conditions. However, the introduction of an acidic-aromatic sensing region in the β-barrel dramatically increased the dwell time and the discrimination of peptides in the nanopore at acidic pH. Surprisingly, despite the fact that the two β-barrel nanopores have a similar diameter and an acidic-aromatic construction, their capture mechanisms differ. The electro-osmotic flow played a dominant role for aerolysin, while the electrophoretic force dominated for cytotoxin K. Nonetheless, both β-barrel nanopores allowed the detection of mixtures of trypsinated peptides, with aerolysin nanopores showing a better resolution for larger peptides and cytotoxin K showing a better resolution for shorter peptides. Therefore, this work provides a generic strategy for modifying nanopores for peptide detection that will be most likely be applicable to other nanopore-forming toxins.
Collapse
Affiliation(s)
| | | | - Gemma Stouwie
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| |
Collapse
|
12
|
Hasegawa N, Shoji K. Microcavity volume control on a tip of Ag/AgCl electrodes for stable channel current measurements of biological nanopores. Analyst 2022; 147:1191-1198. [PMID: 35195650 DOI: 10.1039/d2an00014h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A probe-type channel current measurement system with a planer bilayer lipid membrane (pBLM) at the tip of a probe provided several advantages for pBLM formation and channel current measurements. The procedure for preparing pBLMs was simple (i.e., the probe was submerged into a bath solution layered by an oil/lipid mixture and buffer solution). The probe systems offered local detection of analytes by nanopore sensing. Nevertheless, the current decay caused by changing the ion concentration in the electrolyte held on the tip of the probes influenced the sensing accuracy. Here we applied a cavity microelectrode (CME) technique to fabricate pBLM probes with larger electrolyte volume on the tip. We fabricated silver CMEs with different cavity volumes and measured channel currents of biological nanopores. Furthermore, we evaluated the channel current decay as a function of cavity volume by analyzing the step signals of α-hemolysin nanopores. Consequently, the channel current decay was extended by increasing the cavity volume, indicating that the volume of the electrolyte solution was important for channel current measurements of nanopores. We concluded that the pBLM system using CMEs is useful for channel current measurements of biological nanopores. Additionally, the fundamental evaluation of the relationship between the electrolyte volume and channel current decay will be helpful in the design of pBLM systems made by microfabrication and microfluidic techniques.
Collapse
Affiliation(s)
- Naru Hasegawa
- Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
| | - Kan Shoji
- Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
| |
Collapse
|
13
|
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.
Collapse
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
| | | |
Collapse
|
14
|
Abstract
Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification. Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.
Collapse
|
15
|
Nanodiagnostics: A review of the medical capabilities of nanopores. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102425. [PMID: 34174420 DOI: 10.1016/j.nano.2021.102425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/22/2021] [Accepted: 05/09/2021] [Indexed: 11/20/2022]
Abstract
Modern diagnostics strive to be accurate, fast, and inexpensive in addition to properly identifying the presence of a disease, infection, or illness. Early diagnosis is key; catching a disease in its early stages can be the difference between fatality and treatment. The challenge with many diseases is that detectability of the disease scales with disease progression. Since single molecule sensors, e.g., nanopores, can sense biomolecules at low concentrations, they have the potential to become clinically relevant in many of today's medical settings. With nanopore-based sensing, lower volumes and concentrations are required for detection, enabling it to be clinically beneficial. Other advantages to using nanopores include that they are tunable to an enormous variety of molecules and boast low costs, and fabrication is scalable for manufacturing. We discuss previous reports and the potential for incorporating nanopores into the medical field for early diagnostics, therapeutic monitoring, and identifying relapse/recurrence.
Collapse
|
16
|
Lucas FR, Sarthak K, Lenting EM, Coltan D, van der Heide NJ, Versloot RCA, Aksimentiev A, Maglia G. The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition. ACS NANO 2021; 15:9600-9613. [PMID: 34060809 PMCID: PMC8223486 DOI: 10.1021/acsnano.0c09958] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/21/2021] [Indexed: 05/21/2023]
Abstract
The detection of analytes and the sequencing of DNA using biological nanopores have seen major advances over recent years. The analysis of proteins and peptides with nanopores, however, is complicated by the complex physicochemical structure of polypeptides and the lack of understanding of the mechanism of capture and recognition of polypeptides by nanopores. In this work, we show that introducing aromatic amino acids at precise positions within the lumen of α-helical fragaceatoxin C (FraC) nanopores increased the capture frequency of peptides and largely improved the discrimination among peptides of similar size. Molecular dynamics simulations determined the sensing region of the nanopore, elucidated the microscopic mechanism enabling accurate characterization of the peptides via ionic current blockades in FraC, and characterized the effect of the pore modification on peptide discrimination. This work provides insights to improve the recognition and to augment the capture of peptides by nanopores, which is important for developing a real-time and single-molecule size analyzer for peptide recognition and identification.
Collapse
Affiliation(s)
| | - Kumar Sarthak
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Erica Mariska Lenting
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David Coltan
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| |
Collapse
|
17
|
Zaitseva E, Obergrussberger A, Weichbrodt C, Boukhet M, Bernhard F, Hein C, Baaken G, Fertig N, Behrends JC. Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers: Next-Generation Instrumentation for Multiple Recordings in Parallel. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2188:67-92. [PMID: 33119847 DOI: 10.1007/978-1-0716-0818-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Artificial lipid bilayers have been used for several decades to study channel-forming pores and ion channels in membranes. Until recently, the classical two-chamber setups have been primarily used for studying the biophysical properties of pore forming proteins. Within the last 10 years, instruments for automated lipid bilayer measurements have been developed and are now commercially available. This chapter focuses on protein purification and reconstitution of channel-forming proteins into lipid bilayers using a classic setup and on the commercially available systems, the Orbit mini and Orbit 16.
Collapse
Affiliation(s)
| | | | | | | | - Frank Bernhard
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
18
|
Piguet F, Ensslen T, Bakshloo MA, Talarimoghari M, Ouldali H, Baaken G, Zaitseva E, Pastoriza-Gallego M, Behrends JC, Oukhaled A. Pore-forming toxins as tools for polymer analytics: From sizing to sequencing. Methods Enzymol 2021; 649:587-634. [PMID: 33712201 DOI: 10.1016/bs.mie.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report here on the nanopore resistive pulse sensing (Np-RPS) method, involving pore-forming toxins as tools for polymer analytics at single molecule level. Np-RPS is an electrical method for the label-free detection of single molecules. A molecule interacting with the pore causes a change of the electrical resistance of the pore, called a resistive pulse, associated with a measurable transient current blockade. The features of the blockades, in particular their depth and duration, contain information on the molecular properties of the analyte. We first revisit the history of Np-RPS, then we discuss the effect of the configuration of the molecule/nanopore interaction on the molecular information that can be extracted from the signal, illustrated in two different regimes that either favor molecular sequencing or molecular sizing. Specifically, we focus on the sizing regime and on the use of two different pore-forming toxins, staphylococcal α-hemolysin (αHL) and aerolysin (AeL) nanopores, for the characterization of water-soluble polymers (poly-(ethylene glycol), (PEG)), homopeptides, and heteropeptides. We discuss how nanopore sizing of polymers could be envisioned as a new approach for peptide/protein sequencing.
Collapse
Affiliation(s)
- Fabien Piguet
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mazdak A Bakshloo
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hadjer Ouldali
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | | | | | - Manuela Pastoriza-Gallego
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany; Freiburg Centre for Materials Research, Freiburg, Germany.
| | - Abdelghani Oukhaled
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
| |
Collapse
|
19
|
Lanphere C, Offenbartl-Stiegert D, Dorey A, Pugh G, Georgiou E, Xing Y, Burns JR, Howorka S. Design, assembly, and characterization of membrane-spanning DNA nanopores. Nat Protoc 2020; 16:86-130. [PMID: 33349702 DOI: 10.1038/s41596-020-0331-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores' chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore-membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2-3 weeks for DNA origami pores.
Collapse
Affiliation(s)
- Conor Lanphere
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Genevieve Pugh
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Elena Georgiou
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| |
Collapse
|
20
|
Chau C, Radford SE, Hewitt EW, Actis P. Macromolecular Crowding Enhances the Detection of DNA and Proteins by a Solid-State Nanopore. NANO LETTERS 2020; 20:5553-5561. [PMID: 32559088 PMCID: PMC7357865 DOI: 10.1021/acs.nanolett.0c02246] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Indexed: 05/19/2023]
Abstract
Nanopore analysis of nucleic acid is now routine, but detection of proteins remains challenging. Here, we report the systematic characterization of the effect of macromolecular crowding on the detection sensitivity of a solid-state nanopore for circular and linearized DNA plasmids, globular proteins (β-galactosidase), and filamentous proteins (α-synuclein amyloid fibrils). We observe a remarkable ca. 1000-fold increase in the molecule count for the globular protein β-galactosidase and a 6-fold increase in peak amplitude for plasmid DNA under crowded conditions. We also demonstrate that macromolecular crowding facilitates the study of the topology of DNA plasmids and the characterization of amyloid fibril preparations with different length distributions. A remarkable feature of this method is its ease of use; it simply requires the addition of a macromolecular crowding agent to the electrolyte. We therefore envision that macromolecular crowding can be applied to many applications in the analysis of biomolecules by solid-state nanopores.
Collapse
Affiliation(s)
- Chalmers
C. Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric W. Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| |
Collapse
|
21
|
Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
Collapse
Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| |
Collapse
|
22
|
Acharya S, Jiang A, Kuo C, Nazarian R, Li K, Ma A, Siegal B, Toh C, Schmidt JJ. Improved Measurement of Proteins Using a Solid-State Nanopore Coupled with a Hydrogel. ACS Sens 2020; 5:370-376. [PMID: 31965788 DOI: 10.1021/acssensors.9b01928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although resistive pulse sensing using solid-state nanopores is capable of single-molecule sensitivity, previous work has shown that nanoparticles, such as proteins, pass through nanopores too quickly for accurate detection with typical measurement apparatus. As a result, nanopore measurements of these particles significantly deviate from theoretically estimated current amplitudes and detection rates. Here, we show that a hydrogel placed on the distal side of a nanopore can increase the residence time of nanoparticles within the nanopore, significantly increasing the detection rate and allowing improved resolution of blockage currents. The method is simple and inexpensive to implement while being label-free and applicable to a wide range of nanoparticle targets. Using hydrogel-backed nanopores, we detected the protein IgG with event frequencies several orders of magnitude higher than those in the absence of the hydrogel and with larger measured currents that agree well with theoretical models. We also show that the improved measurement also enables discrimination of IgG and bovine serum albumin in a mixed solution. Finally, we show that measurements of IgG with the hydrogel-backed nanopores can also yield current amplitude distributions that can be analyzed to infer its approximate shape.
Collapse
Affiliation(s)
- Shiv Acharya
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Ann Jiang
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Chance Kuo
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Reyhaneh Nazarian
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Katharine Li
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Anthony Ma
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Brian Siegal
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Christopher Toh
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Jacob J. Schmidt
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| |
Collapse
|
23
|
Ramm F, Dondapati SK, Thoring L, Zemella A, Wüstenhagen DA, Frentzel H, Stech M, Kubick S. Mammalian cell-free protein expression promotes the functional characterization of the tripartite non-hemolytic enterotoxin from Bacillus cereus. Sci Rep 2020; 10:2887. [PMID: 32076011 PMCID: PMC7031377 DOI: 10.1038/s41598-020-59634-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/23/2020] [Indexed: 11/29/2022] Open
Abstract
Bacillus cereus is increasingly recognized as an opportunistic pathogen causing local and systemic infections. The causative strains typically produce three pore-forming enterotoxins. This study focusses on the tripartite non-hemolytic enterotoxin (Nhe). Until today, studies have tried to elucidate the structure, complex formation and cell binding mechanisms of the tripartite Nhe toxin. Here, we demonstrate the synthesis of the functional tripartite Nhe toxin using eukaryotic cell-free systems. Single subunits, combinations of two Nhe subunits as well as the complete tripartite toxin were tested. Functional activity was determined by hemolytic activity on sheep blood agar plates, planar lipid bilayer measurements as well as cell viability assessment using the MTT assay. Our results demonstrate that cell-free protein synthesis based on translationally active eukaryotic lysates is a platform technology for the fast and efficient synthesis of functionally active, multicomponent toxins.
Collapse
Affiliation(s)
- Franziska Ramm
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Doreen Anja Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Hendrik Frentzel
- German Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany. .,Faculty of Health Sciences, joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
| |
Collapse
|
24
|
Ouldali H, Sarthak K, Ensslen T, Piguet F, Manivet P, Pelta J, Behrends JC, Aksimentiev A, Oukhaled A. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat Biotechnol 2020; 38:176-181. [PMID: 31844293 PMCID: PMC7008938 DOI: 10.1038/s41587-019-0345-2] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 10/18/2019] [Accepted: 11/06/2019] [Indexed: 02/04/2023]
Abstract
Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.
Collapse
Affiliation(s)
- Hadjer Ouldali
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabien Piguet
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
- DreamPore S.A.S., 33 Boulevard du Port 95000, Cergy, France
| | - Philippe Manivet
- APHP, GHU APHP.Nord, DMU BioGem, Hôpital Lariboisière, BIOBANK Lariboisière Department BB-0033-00064, Plateforme de BioPathologie et de Technologies Innovantes en Santé, Paris, France
- INSERM UMR 1141 "NeuroDiderot", Université de Paris, Paris, France
| | - Juan Pelta
- LAMBE UMR 8587, Université d'Evry-Val-d'Essonne, CNRS, CEA, Université Paris-Saclay, Evry, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Freiburg Materials Research Centre (FMF), University of Freiburg, Freiburg, Germany
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Abdelghani Oukhaled
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France.
| |
Collapse
|
25
|
Zheng T, Baaken G, Behrends JC, Rühe J. Microelectrochemical cell arrays for whole-cell currents recording through ion channel proteins based on trans-electroporation approach. Analyst 2019; 145:197-205. [PMID: 31730143 DOI: 10.1039/c9an01737b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High electrostability and long life-time of planar chip technology are crucial for electrophysiological measurements such as ionic current recording through ion channel proteins embedded in biological cell membrane. In this paper, we propose a novel planar microchip integrated with microelectrochemical cell array toward to a feasible solution for ion channel screening with high resolution and long life-time. In order to reduce the interference from the leakage currents, a synthetic lipid bilayer is applied to form a high sealing resistance. The whole-cell electrical access can be constructed via electroporating the lipid bilayer in close proximity to the cell membrane. Parameters of electroporation including amplitude and time scale are firstly optimized by using parallel electroporation to the lipid bilayers. In this approach, individual cells can be trapped to the target positions by applying dielectrophoresis (DEP) manipulation. Poly(ethylene glycol) (PEG) is employed with low concentration to facilitate the closed contact between the cells and the lipid bilayer to increase the efficiency of the whole-cell mode construction. Through this chip based method, stable current recordings through inward rectifier potassium (Kir) ion channels embedded in rat basophilic leukemia (RBL-1) cell membrane are achieved with high electrical sealing resistance (over 1 GΩ). In addition, without need for complex fluidic connections, this method allows for an easy operation and further miniaturization of the measuring system.
Collapse
Affiliation(s)
- Tianyang Zheng
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, 100084, Beijing, China.
| | | | | | | |
Collapse
|
26
|
Tsutsui M, Yokota K, Arima A, He Y, Kawai T. Solid-State Nanopore Time-of-Flight Mass Spectrometer. ACS Sens 2019; 4:2974-2979. [PMID: 31576750 DOI: 10.1021/acssensors.9b01470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of field-controlled dynamics of ionized substances in a vacuum enables mass spectroscopy of particles and molecules. Analogously, here we report that nanoscale tracking of electrophoretically driven fast motions of single nanoparticles allows label-free and nondestructive detection of their mass in liquid. We fine-traced the time-dependent positions of space-filtered regular motions of particles passed through a thin solid-state nanopore by dissecting the associated ionic blockade phenomena under a scope of multiphysics simulations. Characterizing the viscous-drag-mediated exponential decay in the electrophoretic speed of particles ejected into an electrolyte solution from the nanochannel, we demonstrated the discrimination of nanoparticles by the femtogram mass difference. The present method is viable for mass measurement of virtually any object that can be put through the sensing zone, the sensor capability of which may find many applications such as pathogen screening and proteomics.
Collapse
Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| | - Yuhui He
- Huazhong University of Science and Technology, Wuhan 430074, China
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Osaka, Ibaraki 567-0047, Japan
| |
Collapse
|
27
|
Dondapati SK, Lübberding H, Zemella A, Thoring L, Wüstenhagen DA, Kubick S. Functional Reconstitution of Membrane Proteins Derived From Eukaryotic Cell-Free Systems. Front Pharmacol 2019; 10:917. [PMID: 31543813 PMCID: PMC6728924 DOI: 10.3389/fphar.2019.00917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/22/2019] [Indexed: 11/23/2022] Open
Abstract
Cell-free protein synthesis (CFPS) based on eukaryotic Sf21 lysate is gaining interest among researchers due to its ability to handle the synthesis of complex human membrane proteins (MPs). Additionally Sf21 cell-free systems contain endogenous microsomal vesicles originally derived from the endoplasmic reticulum (ER). After CFPS, MPs will be translocated into the microsomal vesicles membranes present in the lysates. Thus microsomal membranes offer a natural environment for de novo synthesized MPs. Despite the advantage of synthesizing complex MPs with post translational modifications directly into the microsomal membranes without any additional solubilization supplements, batch based Sf21 cell-free synthesis suffers from low yields. The bottleneck for MPs in particular after the synthesis and incorporation into the microsomal membranes is to analyze their functionality. Apart from low yields of the synthesized MPs with batch based cell-free synthesis, the challenges arise in the form of cytoskeleton elements and peripheral endogenous proteins surrounding the microsomes which may impede the functional analysis of the synthesized proteins. So careful sample processing after the synthesis is particularly important for developing the appropriate functional assays. Here we demonstrate how MPs (native and batch synthesized) from ER derived microsomes can be processed for functional analysis by electrophysiology and radioactive uptake assay methods. Treatment of the microsomal membranes either with a sucrose washing step in the case of human serotonin transporter (hSERT) and sarco/endoplasmic reticulum Ca2+/ATPase (SERCA) pump or with mild detergents followed by the preparation of proteoliposomes in the case of the human voltage dependent anionic channel (hVDAC1) helps to analyze the functional properties of MPs.
Collapse
Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Henning Lübberding
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
| |
Collapse
|
28
|
Choi G, Murphy E, Guan W. Microfluidic Time-Division Multiplexing Accessing Resistive Pulse Sensor for Particle Analysis. ACS Sens 2019; 4:1957-1963. [PMID: 31264411 DOI: 10.1021/acssensors.9b01067] [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] [Indexed: 11/29/2022]
Abstract
Due to its simplicity and robustness, pore-based resistive pulse sensors have been widely used to detect, measure, and analyze particles at length scales ranging from nanometers to micrometers. While multiple pore-based resistive pulse sensors are preferred to increase the analysis throughput and to overcome the clogging issues, the scalability is often limited. In response, by combining the time-division multiple access technique in the telecommunication field with the microfluidics, we reported a microfluidic time-division multiplexing accessing (TDMA) single-end resistive pulse sensor, in which particles can be analyzed through a scalable number of microfluidic channels. With an eight-channel microfluidic device and polystyrene particles as proof-of-principle, we successfully demonstrated this multiplexed technology is effective in measuring the particle size and concentration, in analyzing the particle arriving dynamics, and in discriminating mixed populations. Importantly, the availability of multiple sensing pores provides a robust mechanism to overcome the clogging issue, allowing the analysis to continue even when some of the pores are clogged. We anticipate this TDMA approach could find wide applications and facilitate future development of multiplexed resistive pulse sensing from the microscale to nanoscale.
Collapse
Affiliation(s)
- Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Erica Murphy
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
29
|
Wang H, Kasianowicz JJ, Robertson JWF, Poster DL, Ettedgui J. A comparison of ion channel current blockades caused by individual poly(ethylene glycol) molecules and polyoxometalate nanoclusters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:83. [PMID: 31250227 DOI: 10.1140/epje/i2019-11838-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous nanometer-scale pores have been used to detect and physically characterize many different types of analytes at the single-molecule limit. The method is based on the ability to measure the transient reduction in the ionic channel conductance caused by molecules that partition into the pore. The distribution of blockade depth amplitudes and residence times of the analytes in the pore are used to physically and chemically characterize them. Here we compare the current blockade events caused by flexible linear polymers of ethylene glycol (PEGs) and structurally well-defined tungsten polyoxymetallate nanoparticles in the nanopores formed by Staphylococcus aureusα-hemolysin and Aeromonas hydrophila aerolysin. Surprisingly, the variance in the ionic current blockade depth values for the relatively rigid metallic nanoparticles is much greater than that for the flexible PEGs, possibly because of multiple charged states of the polyoxymetallate clusters.
Collapse
Affiliation(s)
- Haiyan Wang
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Shenzhen Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, 508060, Shenzhen, China
| | - John J Kasianowicz
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA.
- Columbia University, Department of Applied Physics Applied Mathematics, 10027, New York, NY, USA.
| | - Joseph W F Robertson
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Dianne L Poster
- National Institute of Standards and Technology, Material Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Jessica Ettedgui
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Columbia University, Department of Chemical Engineering, 10027, New York, NY, USA
| |
Collapse
|
30
|
Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
Collapse
Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| |
Collapse
|
31
|
Amayreh M, Baaken G, Behrends JC, Manoli Y. A Fully Integrated Current-Mode Continuous-Time Delta-Sigma Modulator for Biological Nanopore Read Out. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2019; 13:225-236. [PMID: 30582552 DOI: 10.1109/tbcas.2018.2889536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This paper presents a fully integrated low noise current-to-digital converter based on current-mode continuous-time delta-sigma modulators (CT DSMs). The circuit was realized in standard 0.35 μm complimentary metal-oxide-semiconductor process and achieves a noise floor as low as 200 fA rms within a bandwidth of 10 kHz. Thanks to the continuous-time architecture, the oversampling together with the implicit anti-aliasing behavior of the current-mode CT DSM prevents the back folding of any out-of-band signals and noises. Running at a sampling frequency of 1.6 MHz, the circuit achieves a measured worst case anti-aliasing filtering of -110 dB for an out-of-band signal at 1.59 MHz. This characteristic eliminates the need of an anti-aliasing filter, which reduces the complexity as well as the area and power consumption. Two feedback versions, a transistor based as well as a capacitor-based current division have been used to reduce the reference current noise. The transistor-based current division feedback modulator consumes a power of 6.73 mW and occupies an area of 0.63 mm 2, whereas the capacitor based consumes a power of 4.6 mW and occupies an area of 0.32 mm 2. Both of them operate at a supply voltage of ±1.5 V.
Collapse
|
32
|
Li X, Zhang T, Gao P, Wei B, Jia Y, Cheng Y, Lou X, Xia F. Integrated Solid-State Nanopore Electrochemistry Array for Sensitive, Specific, and Label-Free Biodetection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14787-14795. [PMID: 30130405 DOI: 10.1021/acs.langmuir.8b02010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanopore ionic current measurement is currently a prevailing readout and offers considerable opportunities for bioassays. Extending conventional electrochemistry to nanoscale space, albeit noteworthy, remains challenging. Here, we report a versatile electrochemistry array established on a nanofluidic platform by controllably depositing gold layers on the two outer sides of anodic aluminum oxide (AAO) nanopores, leading to form an electrochemical microdevice capable of performing amperometry in a label-free manner. Electroactive species ferricyanide ions passing through gold-decorated nanopores act as electrochemical indicator to generate electrolytic current signal. The electroactive species flux that dominates current signal response is closely related to the nanopore permeability. Such well-characteristic electrolytic current-species flux correlation lays a premise for quantitative electrochemical analysis. As a proof-of-concept demonstration, we preliminarily verify the analytical utility by detection of nucleic acid and protein at picomolar concentration levels. Universal surface modification and molecule assembly, specific target recognition and reliable signal output in nanopore enable direct electrochemical detection of biomolecules without the need of cumbersome probe labeling and signal amplification.
Collapse
Affiliation(s)
- Xinchun Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
- Pharmacuetical Analysis Division, School of Pharmacy , Guangxi Medical University , 22 Shuangyong Road , Nanning 530021 , People's Republic of China
| | - Tianchi Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
| | - Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , 388 Lumo Road , Wuhan 430074 , People's Republic of China
| | - Benmei Wei
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
| | - Yongmei Jia
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
| | - Yong Cheng
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , 388 Lumo Road , Wuhan 430074 , People's Republic of China
| | - Fan Xia
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , People's Republic of China
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , 388 Lumo Road , Wuhan 430074 , People's Republic of China
| |
Collapse
|
33
|
The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin. Biophys J 2018; 115:1720-1730. [PMID: 30287110 DOI: 10.1016/j.bpj.2018.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 01/25/2023] Open
Abstract
Molecular dynamics simulations were performed to describe the function of the ion-channel-forming toxin α-hemolysin (αHL) in lipid membranes that were composed of either 1,2-diphytanoyl-sn-glycero-3-phospho-choline or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline. The simulations highlight the importance of lipid type in maintaining αHL structure and function, enabling direct comparison to experiments for biosensing applications. We determined that although the two lipids studied are similar in structure, 1,2-diphytanoyl-sn-glycero-3-phospho-choline membranes better match the hydrophobic thickness of αHL compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline membranes. This hydrophobic match is essential to maintaining proper alignment of β-sheet loops at the trans entrance of αHL, which, when disrupted, creates an additional constriction to ion flow that decreases the channel current below experimental values and creates greater variability in channel conductance. Agreement with experiments was further improved with sufficient lipid membrane equilibration and allowed the discrimination of subtle αHL conduction states with lipid type. Finally, we explore the effects of truncating the extramembrane cap of αHL and its role in maintaining proper alignment of αHL in the membrane and channel conductance. Our results demonstrate the essential role of lipid type and lipid-protein interactions in simulations of αHL and will considerably improve the interpretation of experimental data.
Collapse
|
34
|
Roman J, Le Pioufle B, Auvray L, Pelta J, Bacri L. From current trace to the understanding of confined media. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:99. [PMID: 30159758 DOI: 10.1140/epje/i2018-11709-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Nanopores constitute devices for the sensing of nano-objects such as ions, polymer chains, proteins or nanoparticles. We describe what information we can extract from the current trace. We consider the entrance of polydisperse chains into the nanopore, which leads to a conductance drop. We describe the detection of these current blockades according to their shape. Finally, we explain how data analysis can be used to enhance our understanding of physical processes in confined media.
Collapse
Affiliation(s)
- Jean Roman
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France
| | - Bruno Le Pioufle
- ENS Paris-Saclay, CNRS, Institut d'Alembert, SATIE, Université Paris-Saclay, F-94230, Cachan, France
| | - Loïc Auvray
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
| | - Juan Pelta
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France
| | - Laurent Bacri
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France.
| |
Collapse
|
35
|
Talarimoghari M, Baaken G, Hanselmann R, Behrends JC. Size-dependent interaction of a 3-arm star poly(ethylene glycol) with two biological nanopores. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:77. [PMID: 29926213 DOI: 10.1140/epje/i2018-11687-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
We use two pore-forming proteins, alpha-hemolysin and aerolysin, to compare the polymer size-dependence of ionic current block by two types of ethyleneglycol polymers: 1) linear and 2) 3-arm star poly(ethylene glycol), both applied as a polydisperse mixture of average mass 1kDa under high salt conditions. The results demonstrate that monomer size sensitivity, as known for linear PEGs, is conserved for the star polymers with only subtle differences in the dependence of the residual conductance on monomer number. To explain this absence of a dominant effect of polymer architecture, we propose that PEG adsorbs to the inner pore wall in a collapsed, salted-out state, likely due to the effect of hydrophobic residues in the pore wall on the availability of water for hydration.
Collapse
Affiliation(s)
- Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Gerhard Baaken
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Ralf Hanselmann
- Institute for Macromolecular Chemistry, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany.
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany.
- Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
| |
Collapse
|
36
|
Diederichs T, Nguyen QH, Urban M, Tampé R, Tornow M. Transparent Nanopore Cavity Arrays Enable Highly Parallelized Optical Studies of Single Membrane Proteins on Chip. NANO LETTERS 2018; 18:3901-3910. [PMID: 29741381 DOI: 10.1021/acs.nanolett.8b01252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Membrane proteins involved in transport processes are key targets for pharmaceutical research and industry. Despite continuous improvements and new developments in the field of electrical readouts for the analysis of transport kinetics, a well-suited methodology for high-throughput characterization of single transporters with nonionic substrates and slow turnover rates is still lacking. Here, we report on a novel architecture of silicon chips with embedded nanopore microcavities, based on a silicon-on-insulator technology for high-throughput optical readouts. Arrays containing more than 14 000 inverted-pyramidal cavities of 50 femtoliter volumes and 80 nm circular pore openings were constructed via high-resolution electron-beam lithography in combination with reactive ion etching and anisotropic wet etching. These cavities feature both, an optically transparent bottom and top cap. Atomic force microscopy analysis reveals an overall extremely smooth chip surface, particularly in the vicinity of the nanopores, which exhibits well-defined edges. Our unprecedented transparent chip design provides parallel and independent fluorescent readout of both cavities and buffer reservoir for unbiased single-transporter recordings. Spreading of large unilamellar vesicles with efficiencies up to 96% created nanopore-supported lipid bilayers, which are stable for more than 1 day. A high lipid mobility in the supported membrane was determined by fluorescent recovery after photobleaching. Flux kinetics of α-hemolysin were characterized at single-pore resolution with a rate constant of 0.96 ± 0.06 × 10-3 s-1. Here, we deliver an ideal chip platform for pharmaceutical research, which features high parallelism and throughput, synergistically combined with single-transporter resolution.
Collapse
Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
| | - Quoc Hung Nguyen
- Molecular Electronics , Technical University of Munich , Theresienstrasse 90 , 80333 Munich , Germany
| | - Michael Urban
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/M. , Germany
- Cluster of Excellence Frankfurt (CEF) Macromolecular Complexes ; Goethe University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt/M. , Germany
| | - Marc Tornow
- Molecular Electronics , Technical University of Munich , Theresienstrasse 90 , 80333 Munich , Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT) , Hansastrasse 27d , 80686 Munich , Germany
- Center for NanoScience (CeNS) , Ludwig-Maximilians-University , Geschwister-Scholl Platz 1 , 80539 Munich , Germany
| |
Collapse
|
37
|
Abstract
Cell-free production is a valuable and alternative method for the synthesis of membrane proteins. This system offers openness allowing the researchers to modify the reaction conditions without any boundaries. Additionally, the cell-free reactions are scalable from 20 μL up to several mL, faster and suitable for the high-throughput protein production. Here, we present two cell-free systems derived from Escherichia coli (E. coli) and Spodoptera frugiperda (Sf21) lysates. In the case of the E. coli cell-free system, nanodiscs are used for the solubilization and purification of membrane proteins. In the case of the Sf21 system, endogenous microsomes with an active translocon complex are present within the lysates which facilitate the incorporation of the bacterial potassium channel KcsA within the microsomal membranes. Following cell-free synthesis, these microsomes are directly used for the functional analysis of membrane proteins.
Collapse
|
38
|
Coglitore D, Merenda A, Giamblanco N, Dumée LF, Janot JM, Balme S. Metal alloy solid-state nanopores for single nanoparticle detection. Phys Chem Chem Phys 2018; 20:12799-12807. [PMID: 29697724 DOI: 10.1039/c8cp01787e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Solid-state nanopore technology for nanoparticle sensing is considered for the development of analytical tools to characterise their size, shape or zeta potential. In this field, it is crucial to understand how the nanopore inner surface influences the dynamic of nanoparticle translocation. Here, three single nanopores directly drilled in metal alloys (titanium nitride, titanium-tantalum and tantalum) are considered. The translocation of polystyrene nanoparticles coated with ssDNA is investigated by the resistive pulse method at different concentrations and voltages. The results show that the nanoparticle energy barrier for entrance into the pore decreases for nanopores that exhibits a higher surface energy and hydrophilicity, while the dwell time is found to depend on the nanopore surface state. Overall, this study demonstrates that the control of nanopore surface state must be taken into account for the resistive pulse experiments for nanoparticle detection.
Collapse
Affiliation(s)
- Diego Coglitore
- Institut Européen des Membranes, UMR5635, Université de Montpellier CNRS ENSCM, Place Eugène Bataillon, 34090 Montpellier, France.
| | | | | | | | | | | |
Collapse
|
39
|
Booth MJ, Restrepo Schild V, Downs FG, Bayley H. Functional aqueous droplet networks. MOLECULAR BIOSYSTEMS 2018; 13:1658-1691. [PMID: 28766622 DOI: 10.1039/c7mb00192d] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Droplet interface bilayers (DIBs), comprising individual lipid bilayers between pairs of aqueous droplets in an oil, are proving to be a useful tool for studying membrane proteins. Recently, attention has turned to the elaboration of networks of aqueous droplets, connected through functionalized interface bilayers, with collective properties unachievable in droplet pairs. Small 2D collections of droplets have been formed into soft biodevices, which can act as electronic components, light-sensors and batteries. A substantial breakthrough has been the development of a droplet printer, which can create patterned 3D droplet networks of hundreds to thousands of connected droplets. The 3D networks can change shape, or carry electrical signals through defined pathways, or express proteins in response to patterned illumination. We envisage using functional 3D droplet networks as autonomous synthetic tissues or coupling them with cells to repair or enhance the properties of living tissues.
Collapse
Affiliation(s)
- Michael J Booth
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | | | | | | |
Collapse
|
40
|
Wang H, Ettedgui J, Forstater J, Robertson JWF, Reiner JE, Zhang H, Chen S, Kasianowicz JJ. Determining the Physical Properties of Molecules with Nanometer-Scale Pores. ACS Sens 2018; 3:251-263. [PMID: 29381331 DOI: 10.1021/acssensors.7b00680] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nanometer-scale pores have been developed for the detection, characterization, and quantification of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles) and for DNA sequencing. We describe the key requirements that made this method possible and how the technique evolved. Finally, we show that, despite sound theoretical work, which advanced both the conceptual framework and quantitative capability of the method, there are still unresolved questions that need to be addressed to further improve the technique.
Collapse
Affiliation(s)
- Haiyan Wang
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Jessica Ettedgui
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Jacob Forstater
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Joseph W. F. Robertson
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Huisheng Zhang
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Siping Chen
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - John J. Kasianowicz
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Applied Physics Applied Mathematics, Columbia University New York, New York 10027, United States
| |
Collapse
|
41
|
Figueiredo PG, Grob L, Rinklin P, Krause KJ, Wolfrum B. On-Chip Stochastic Detection of Silver Nanoparticles without a Reference Electrode. ACS Sens 2018; 3:93-98. [PMID: 29276833 DOI: 10.1021/acssensors.7b00559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the electrochemical detection of 20 nm silver nanoparticles at a chip-based microelectrode array (MEA) without the need for a conventional reference electrode. This is possible due to the system's open-circuit potential allowing the oxidation of silver nanoparticles in the presence of phosphate-buffered saline (PBS). The hypothesis is confirmed by modulating the open-circuit potential via addition of ascorbic acid in solution, effectively inhibiting the detection of silver nanoparticle events. Employing the reference-free detection concept, we observe a linear relationship between the nanoparticle impact frequency at the microelectrodes and the nanoparticle concentration. This allows for viable quantification of silver nanoparticle concentrations in situ. The presented concept is ideal for the development of simple lab-on-a-chip or point-of-use systems enabling fast and low-cost screening of nanoparticles.
Collapse
Affiliation(s)
- Pedro G. Figueiredo
- Neuroelectronics
- Munich School of Bioengineering, Department of Electrical and Computer
Engineering, Technical University of Munich, Boltzmannstraße 11, D-85749, Garching, Germany
| | - Leroy Grob
- Neuroelectronics
- Munich School of Bioengineering, Department of Electrical and Computer
Engineering, Technical University of Munich, Boltzmannstraße 11, D-85749, Garching, Germany
| | - Philipp Rinklin
- Neuroelectronics
- Munich School of Bioengineering, Department of Electrical and Computer
Engineering, Technical University of Munich, Boltzmannstraße 11, D-85749, Garching, Germany
| | - Kay J. Krause
- Niederrhein University of Applied Science, Department
of Food Science and Nutrition, Rheydter Str. 277, 41065 Mönchengladbach, Germany
| | - Bernhard Wolfrum
- Neuroelectronics
- Munich School of Bioengineering, Department of Electrical and Computer
Engineering, Technical University of Munich, Boltzmannstraße 11, D-85749, Garching, Germany
- Institute
of Complex Systems ICS-8, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
42
|
Balme S, Picaud F, Lepoitevin M, Bechelany M, Balanzat E, Janot JM. Unexpected ionic transport behavior in hydrophobic and uncharged conical nanopores. Faraday Discuss 2018; 210:69-85. [DOI: 10.1039/c8fd00008e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated ionic transport behavior in the case of uncharged conical nanopores. We observed unexpected ionic transport behaviour, which is attributed to a predominant effect of slippage due to water organization at the solid/liquid interface.
Collapse
Affiliation(s)
- Sebastien Balme
- Institut Européen des Membranes
- IEM – UMR 5635
- ENSCM
- CNRS
- Univ. Montpellier
| | - Fabien Picaud
- Laboratoire de Nanomédecine
- Imagerie et Thérapeutique, EA 4662
- Université Bourgogne Franche-Comté
- Centre Hospitalier Universitaire de Besançon
- 25030 Besançon cedex
| | | | - Mikhael Bechelany
- Institut Européen des Membranes
- IEM – UMR 5635
- ENSCM
- CNRS
- Univ. Montpellier
| | - Emmanuel Balanzat
- Centre de recherche sur les Ions
- les Matériaux et la Photonique
- UMR6252 CEA-CNRS-ENSICAEN
- France
| | - Jean-Marc Janot
- Institut Européen des Membranes
- IEM – UMR 5635
- ENSCM
- CNRS
- Univ. Montpellier
| |
Collapse
|
43
|
Dondapati SK, Wüstenhagen DA, Strauch E, Kubick S. Cell-free production of pore forming toxins: Functional analysis of thermostable direct hemolysin from Vibrio parahaemolyticus. Eng Life Sci 2017; 18:140-148. [PMID: 29497355 PMCID: PMC5814925 DOI: 10.1002/elsc.201600259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 09/19/2017] [Accepted: 11/02/2017] [Indexed: 01/21/2023] Open
Abstract
The pore forming characteristic of TDH1 and TDH2 variants of thermostable direct hemolysin (TDH), a major toxin involved in the pathogenesis of Vibrio parahaemolyticus, was studied on a planar lipid bilayer painted over individual picoliter cavities containing microelectrodes assembled in a multiarray. Both proteins formed pores upon insertion into the lipid bilayer which was shown as a shift in the conductance from the baseline current. TDH2 protein was able to produce stable currents and the currents were influenced by external factors like concentration, type of salt and voltage. The pore currents were influenced and showed a detectable response in the presence of polymers which makes them suitable for biotechnology applications.
Collapse
Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Eckhard Strauch
- Federal Institute for Risk Assessment Department of Biological Safety National Reference Laboratory for Monitoring Bacteriological Contamination of Bivalve Molluscs Berlin Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| |
Collapse
|
44
|
Jain T, Rasera BC, Guerrero RJS, Lim JM, Karnik R. Microfluidic multiplexing of solid-state nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:484001. [PMID: 29116942 DOI: 10.1088/1361-648x/aa9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although solid-state nanopores enable electronic analysis of many clinically and biologically relevant molecular structures, there are few existing device architectures that enable high-throughput measurement of solid-state nanopores. Herein, we report a method for microfluidic integration of multiple solid-state nanopores at a high density of one nanopore per (35 µm2). By configuring microfluidic devices with microfluidic valves, the nanopores can be rinsed from a single fluid input while retaining compatibility for multichannel electrical measurements. The microfluidic valves serve the dual purpose of fluidic switching and electric switching, enabling serial multiplexing of the eight nanopores with a single pair of electrodes. Furthermore, the device architecture exhibits low noise and is compatible with electroporation-based in situ nanopore fabrication, providing a scalable platform for automated electronic measurement of a large number of integrated solid-state nanopores.
Collapse
Affiliation(s)
- Tarun Jain
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, United States of America
| | | | | | | | | |
Collapse
|
45
|
Lutz JF. Defining the Field of Sequence-Controlled Polymers. Macromol Rapid Commun 2017; 38. [PMID: 29160615 DOI: 10.1002/marc.201700582] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/13/2017] [Indexed: 12/31/2022]
Abstract
Over the last ten years, the development of synthetic polymers containing controlled monomer sequences has become a prominent topic in fundamental and applied polymer science. This emerging area is particularly broad and combines classical polymer chemistry tools with techniques imported from other domains such as biology, biochemistry, organic synthesis, engineering, and bioanalytics. Consequently, it also generates new structures, terminologies, and applications that are not within the traditional scope of polymer science. The term "sequence-controlled polymers" (SCPs) was recently proposed as a generic name to describe all these recent trends. However, since the field of SCPs has been growing very rapidly in recent literature, it is urgent to accurately define its scientific frontiers. In this important context, this review is an attempt to define, rationalize, and classify the field of SCPs. In particular, all synthetic approaches that have been reported for the synthesis of SCPs are discussed and categorized. In addition, the characterization tools, properties, and potential applications of these new polymers are described herein. Overall, this review serves as a reference guide for understanding the burgeoning field of SCPs.
Collapse
Affiliation(s)
- Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| |
Collapse
|
46
|
Boukhet M, König NF, Ouahabi AA, Baaken G, Lutz JF, Behrends JC. Translocation of Precision Polymers through Biological Nanopores. Macromol Rapid Commun 2017; 38. [PMID: 29144014 DOI: 10.1002/marc.201700680] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/25/2017] [Indexed: 11/10/2022]
Abstract
Nanopore analysis, which is, currently, chiefly used for DNA sequencing, is also an appealing technique for characterizing abiotic polymers. As a first step toward this goal, nanopore detection of non-natural monodispersed poly(phosphodiester)s as candidate backbone structures is reported herein. Two model homopolymers containing phosphopropyl repeat units (i.e., 56 or 104 r.u.) and a short thymidine nucleotide sequence are analyzed in the present work. They are tested in two different biological nanopores, α-hemolysin from Staphylococcus aureus, and aerolysin from Aeromonas hydrophila. These recordings are performed in aqueous medium at different KCl concentrations and various driving voltages. The data show a complex interaction with evidence for voltage dependence and threading, and underline the influence of the molecular structure and orientation of the precision poly(phosphodiester)s on the observed residual current signal as well as on the translocation dynamics. In particular, they suggest a dominant entropic contribution due to the high flexibility of the phosphodiester homopolymer.
Collapse
Affiliation(s)
- Mordjane Boukhet
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Niklas Felix König
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 Rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Abdelaziz Al Ouahabi
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 Rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Gerhard Baaken
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Jean-François Lutz
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 Rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany.,Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany.,Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
| |
Collapse
|
47
|
Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 PMCID: PMC11274829 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
Collapse
Affiliation(s)
- Amy E. Chavis
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph W. F. Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
48
|
Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nat Protoc 2017; 12:1901-1911. [PMID: 28837133 DOI: 10.1038/nprot.2017.077] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nanopore techniques offer the possibility to study biomolecules at the single-molecule level in a low-cost, label-free and high-throughput manner. By analyzing the level, duration and frequency of ionic current blockades, information regarding the structural conformation, mass, length and concentration of single molecules can be obtained in physiological conditions. Aerolysin monomers assemble into small pores that provide a confined space for effective electrochemical control of a single molecule interacting with the pore, which significantly improves the temporal resolution of this technique. In comparison with other reported protein nanopores, aerolysin maintains its functional stability in a wide range of pH conditions, which allows for the direct discrimination of oligonucleotides between 2 and 10 nt in length and the monitoring of the stepwise cleavage of oligonucleotides by exonuclease I (Exo I) in real time. This protocol describes the process of activating proaerolysin using immobilized trypsin to obtain the aerolysin monomer, the construction of a lipid membrane and the insertion of an individual aerolysin nanopore into this membrane. A step-by-step description is provided of how to perform single-oligonucleotide analyses and how to process the acquired data. The total time required for this protocol is ∼3 d.
Collapse
|
49
|
Neveshkin A, Citak F, Ball V, Winterhalter M. Polydopamine Coating To Stabilize a Free-Standing Lipid Bilayer for Channel Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7256-7262. [PMID: 28657327 DOI: 10.1021/acs.langmuir.7b01959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An appropriate method to study the function of membrane channels is to insert them into free-standing lipid bilayers and to record the ion conductance across the membrane. The insulating property of a free-standing lipid bilayer versus the single-channel conductivity provides sufficient sensitivity to detect minor changes in the pathway of ions along the channel. A potential application is to use membrane channels as label-free sensors for molecules, with DNA sequencing as its most prominent application. However, the inherent instability of free-standing bilayers limits broader use as a biosensor. Here we report on a possible stabilization of free-standing lipid bilayers using polydopamine deposition from dopamine-containing solutions in the presence of an oxidant. This stabilization treatment can be initiated after protein reconstitution and is compatible with most reconstitution protocols.
Collapse
Affiliation(s)
- Alexander Neveshkin
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
- Yuri Gagarin State Technical University of Saratov , 77 Politechnicheskaya Street, Saratov, Russia , 410054
| | - Funda Citak
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
| | - Vincent Ball
- Institut National de la Santé et de la Recherche Médicale , Unité Mixte de Recherche 1121, 11 Rue Humann, 67085 Strasbourg Cedex, France
- Université de Strasbourg, Faculté de Chirurgie Dentaire , 8 Rue Sainte Elisabeth, 67000 Strasbourg, France
| | | |
Collapse
|
50
|
Salnikov ES, Raya J, De Zotti M, Zaitseva E, Peggion C, Ballano G, Toniolo C, Raap J, Bechinger B. Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR. Biophys J 2017; 111:2450-2459. [PMID: 27926846 DOI: 10.1016/j.bpj.2016.09.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022] Open
Abstract
Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C19F3-labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19F-19F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.
Collapse
Affiliation(s)
- Evgeniy S Salnikov
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Jesus Raya
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Ekaterina Zaitseva
- Department of Membrane Physiology and Technology, Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Gema Ballano
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, Leiden, the Netherlands
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France.
| |
Collapse
|