51
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Ruiz-Arroyo VM, García-Robles I, Ochoa-Campuzano C, Goig GA, Zaitseva E, Baaken G, Martínez-Ramírez AC, Rausell C, Real MD. Validation of ADAM10 metalloprotease as a Bacillus thuringiensis Cry3Aa toxin functional receptor in Colorado potato beetle (Leptinotarsa decemlineata). INSECT MOLECULAR BIOLOGY 2017; 26:204-214. [PMID: 27918112 DOI: 10.1111/imb.12285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacillus thuringiensis parasporal crystal proteins (Cry proteins) are insecticidal pore-forming toxins that bind to specific receptor molecules on the brush border membrane of susceptible insect midgut cells to exert their toxic action. In the Colorado potato beetle (CPB), a coleopteran pest, we previously proposed that interaction of Cry3Aa toxin with a CPB ADAM10 metalloprotease is an essential part of the mode of action of this toxin. Here, we annotated the gene sequence encoding an ADAM10 metalloprotease protein (CPB-ADAM10) in the CPB genome sequencing project, and using RNA interference gene silencing we demonstrated that CPB-ADAM10 is a Cry3Aa toxin functional receptor in CPB. Cry3Aa toxicity was significantly lower in CPB-ADAM10 silenced larvae and in vitro toxin pore-forming ability was greatly diminished in lipid planar bilayers fused with CPB brush border membrane vesicles (BBMVs) prepared from CPB-ADAM10 silenced larvae. In accordance with our previous data that indicated this toxin was a substrate of ADAM10 in CPB, Cry3Aa toxin membrane-associated proteolysis was altered when CPB BBMVs lacked ADAM10. The functional validation of CPB-ADAM10 as a Cry3Aa toxin receptor in CPB expands the already recognized role of ADAM10 as a pathogenicity determinant of pore-forming toxins in humans to an invertebrate species.
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Affiliation(s)
- V M Ruiz-Arroyo
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - I García-Robles
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - C Ochoa-Campuzano
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - G A Goig
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - E Zaitseva
- Department of Physiology, University of Freiburg, Freiburg, Germany
- Ionera Technologies GmbH, Freiburg, Germany
| | - G Baaken
- Ionera Technologies GmbH, Freiburg, Germany
| | - A C Martínez-Ramírez
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, Burjassot, Valencia, Spain
| | - C Rausell
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - M D Real
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
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52
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An Automated Microfluidic System for the Generation of Droplet Interface Bilayer Networks. MICROMACHINES 2017. [PMCID: PMC6190347 DOI: 10.3390/mi8030093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Networks of droplets, in which aqueous compartments are separated by lipid bilayers, have shown great potential as a model for biological transmembrane communication. We present a microfluidic system which allows for on-demand generation of droplets that are hydrodynamically locked in a trapping structure. As a result, the system enables the formation of a network of four droplets connected via lipid bilayers and the positions of each droplet in the network can be controlled thanks to automation of microfluidic operations. We perform electrophysiological measurements of ionic currents indicating interactions between nanopores and small molecules to prove the potential of the device in screening of the inhibitors acting on membrane proteins. We also demonstrate, for the first time, a microfluidic droplet interface bilayer (DIB) system in which the testing of inhibitors can be performed without direct contact between the tested sample and the electrodes recording picoampere currents.
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53
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Tahvildari R, Beamish E, Briggs K, Chagnon-Lessard S, Sohi AN, Han S, Watts B, Tabard-Cossa V, Godin M. Manipulating Electrical and Fluidic Access in Integrated Nanopore-Microfluidic Arrays Using Microvalves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602601. [PMID: 28026148 DOI: 10.1002/smll.201602601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
On-chip microvalves regulate electrical and fluidic access to an array of nanopores integrated within microfluidic networks. This configuration allows for on-chip sequestration of biomolecular samples in various flow channels and analysis by independent nanopores.
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Affiliation(s)
- Radin Tahvildari
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Eric Beamish
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Ali Najafi Sohi
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shuo Han
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Benjamin Watts
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Michel Godin
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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54
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Murray KK. Single molecule mass measurements and mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2671-2672. [PMID: 27704625 DOI: 10.1002/rcm.7756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
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55
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Affiliation(s)
- Toshihisa Osaki
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
| | - Shoji Takeuchi
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
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56
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Piguet F, Ouldali H, Discala F, Breton MF, Behrends JC, Pelta J, Oukhaled A. High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore. Sci Rep 2016; 6:38675. [PMID: 27924860 PMCID: PMC5141499 DOI: 10.1038/srep38675] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/11/2016] [Indexed: 01/29/2023] Open
Abstract
We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.
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Affiliation(s)
- Fabien Piguet
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France.,LPTM UMR 8089 CNRS, Cergy University, France
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Faculty of Medicine, Department of Physiology, University of Freiburg, Germany.,Freiburg Materials Research Centre, University of Freiburg, Germany.,Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Germany
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
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57
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Boukhet M, Piguet F, Ouldali H, Pastoriza-Gallego M, Pelta J, Oukhaled A. Probing driving forces in aerolysin and α-hemolysin biological nanopores: electrophoresis versus electroosmosis. NANOSCALE 2016; 8:18352-18359. [PMID: 27762420 DOI: 10.1039/c6nr06936c] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The transport of macromolecules through nanopores is involved in many biological functions and is today at the basis of promising technological applications. Nevertheless the interpretation of the dynamics of the macromolecule/nanopore interaction is still misunderstood and under debate. At the nanoscale, inside biomimetic channels under an external applied voltage, electrophoresis, which is the electric force acting on electrically charged molecules, and electroosmotic flow (EOF), which is the fluid transport associated with ions, contribute to the direction and magnitude of the molecular transport. In order to decipher the contribution of the electrophoresis and electroosmotic flow, we explored the interaction of small, rigid, neutral molecules (cyclodextrins) and flexible, non-ionic polymers (poly(ethylene glycol), PEG) that can coordinate cations under appropriate experimental conditions, with two biological nanopores: aerolysin (AeL) and α-hemolysin (aHL). We performed experiments using two electrolytes with different ionic hydration (KCl and LiCl). Regardless of the nature of the nanopore and of the electrolyte, cyclodextrins behaved as neutral analytes. The dominant driving force was attributed to EOF, acting in the direction of the anion flow and stronger in LiCl than in KCl. The same qualitative behaviour was observed for PEGs in LiCl. In contrast, in KCl, PEGs behaved as positively charged polyelectrolytes through both AeL and aHL. Our results are in agreement with theoretical predictions about the injection of polymers inside a confined geometry (ESI). We believe our results to be of significant importance for better control of the dynamics of analytes of different nature through biological nanopores.
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Affiliation(s)
- Mordjane Boukhet
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | - Fabien Piguet
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | | | - Juan Pelta
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
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58
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Nguyen MA, Srijanto B, Collier CP, Retterer ST, Sarles SA. Hydrodynamic trapping for rapid assembly and in situ electrical characterization of droplet interface bilayer arrays. LAB ON A CHIP 2016; 16:3576-3588. [PMID: 27513561 DOI: 10.1039/c6lc00810k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The droplet interface bilayer (DIB) is a modular technique for assembling planar lipid membranes between water droplets in oil. The DIB method thus provides a unique capability for developing digital, droplet-based membrane platforms for rapid membrane characterization, drug screening and ion channel recordings. This paper demonstrates a new, low-volume microfluidic system that automates droplet generation, sorting, and sequential trapping in designated locations to enable the rapid assembly of arrays of DIBs. The channel layout of the device is guided by an equivalent circuit model, which predicts that a serial arrangement of hydrodynamic DIB traps enables sequential droplet placement and minimizes the hydrodynamic pressure developed across filled traps to prevent squeeze-through of trapped droplets. Furthermore, the incorporation of thin-film electrodes fabricated via evaporation metal deposition onto the glass substrate beneath the channels allows for the first time in situ, simultaneous electrical interrogation of multiple DIBs within a sealed device. Combining electrical measurements with imaging enables measurements of membrane capacitance and resistance and bilayer area, and our data show that DIBs formed in different trap locations within the device exhibit similar sizes and transport properties. Simultaneous, single channel recordings of ion channel gating in multiple membranes are obtained when alamethicin peptides are incorporated into the captured droplets, qualifying the thin-film electrodes as a means for measuring stimuli-responsive functions of membrane-bound biomolecules. This novel microfluidic-electrophysiology platform provides a reproducible, high throughput method for performing electrical measurements to study transmembrane proteins and biomembranes in low-volume, droplet-based membranes.
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Affiliation(s)
- Mary-Anne Nguyen
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, USA.
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59
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KAMIYA K, OSAKI T, TAKEUCHI S. 4.人工細胞膜作製とシングルイオンチャネル計測. ELECTROCHEMISTRY 2015. [DOI: 10.5796/electrochemistry.83.1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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60
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Kasianowicz JJ, Balijepalli AK, Ettedgui J, Forstater JH, Wang H, Zhang H, Robertson JWF. Analytical applications for pore-forming proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:593-606. [PMID: 26431785 DOI: 10.1016/j.bbamem.2015.09.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/28/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023]
Abstract
Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- John J Kasianowicz
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States.
| | | | - Jessica Ettedgui
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Jacob H Forstater
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Haiyan Wang
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Dept. of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
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61
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Affiliation(s)
- William B Dunbar
- Department of Computer Engineering, University of California , Santa Cruz, California 95064, United States
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62
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Gu Z, Ying YL, Cao C, He P, Long YT. Reply to Comment on Accurate Data Process for Nanopore Analysis. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b03225] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhen Gu
- Key Laboratory for Advanced Materials and
Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
- Department
of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials and
Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials and
Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Pingang He
- Department
of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and
Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
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63
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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64
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Lutz JF. Coding Macromolecules: Inputting Information in Polymers Using Monomer-Based Alphabets. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00890] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean-François Lutz
- Precision Macromolecular
Chemistry, Institut Charles Sadron, UPR22-CNRS, 23 rue du Loess, BP84047, 67034 Strasbourg, Cedex
2, France
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65
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Baaken G, Halimeh I, Bacri L, Pelta J, Oukhaled A, Behrends JC. High-Resolution Size-Discrimination of Single Nonionic Synthetic Polymers with a Highly Charged Biological Nanopore. ACS NANO 2015; 9:6443-6449. [PMID: 26028280 DOI: 10.1021/acsnano.5b02096] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Electrophysiological studies of the interaction of polymers with pores formed by bacterial toxins (1) provide a window on single molecule interaction with proteins in real time, (2) report on the behavior of macromolecules in confinement, and (3) enable label-free single molecule sensing. Using pores formed by the staphylococcal toxin α-hemolysin (aHL), a particularly pertinent observation was that, under high salt conditions (3-4 M KCl), the current through the pore is blocked for periods of hundreds of microseconds to milliseconds by poly(ethylene glycol) (PEG) oligomers (degree of polymerization approximately 10-60). Notably, this block showed monomeric sensitivity on the degree of polymerization of individual oligomers, allowing the construction of size or mass spectra from the residual current values. Here, we show that the current through the pore formed by aerolysin (AeL) from Aeromonas hydrophila is also blocked by PEG but with drastic differences in the voltage-dependence of the interaction. In contrast to aHL, AeL strongly binds PEG at high transmembrane voltages. This fact, which is likely related to AeL's highly charged pore wall, allows discrimination of polymer sizes with particularly high resolution. Multiple applications are now conceivable with this pore to screen various nonionic or charged polymers.
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Affiliation(s)
- Gerhard Baaken
- ‡Ionera Technologies GmbH, Hermann Herder Strasse 7, 79104 Freiburg, Germany
| | - Ibrahim Halimeh
- ‡Ionera Technologies GmbH, Hermann Herder Strasse 7, 79104 Freiburg, Germany
| | - Laurent Bacri
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Juan Pelta
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Abdelghani Oukhaled
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Jan C Behrends
- ∥Freiburg Materials Research Centre (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- ⊥Centre for Interactive Materials and Bioinspired Technologies (FIT), Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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66
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Crescentini M, Thei F, Bennati M, Saha S, de Planque MRR, Morgan H, Tartagni M. A Distributed Amplifier System for Bilayer Lipid Membrane (BLM) Arrays With Noise and Individual Offset Cancellation. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2015; 9:334-344. [PMID: 25252284 DOI: 10.1109/tbcas.2014.2346402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Lipid bilayer membrane (BLM) arrays are required for high throughput analysis, for example drug screening or advanced DNA sequencing. Complex microfluidic devices are being developed but these are restricted in terms of array size and structure or have integrated electronic sensing with limited noise performance. We present a compact and scalable multichannel electrophysiology platform based on a hybrid approach that combines integrated state-of-the-art microelectronics with low-cost disposable fluidics providing a platform for high-quality parallel single ion channel recording. Specifically, we have developed a new integrated circuit amplifier based on a novel noise cancellation scheme that eliminates flicker noise derived from devices under test and amplifiers. The system is demonstrated through the simultaneous recording of ion channel activity from eight bilayer membranes. The platform is scalable and could be extended to much larger array sizes, limited only by electronic data decimation and communication capabilities.
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67
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Shi J, Hou J, Fang Y. Recent advances in nanopore-based nucleic acid analysis and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1503-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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68
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Harrach MF, Drossel B. Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity. J Chem Phys 2015; 140:174501. [PMID: 24811640 DOI: 10.1063/1.4872239] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We perform molecular dynamics simulations to observe the structure and dynamics of water using different water models (TIP3P, TIP4P, TIP5P) at ambient conditions, constrained by planar walls, which are either modeled by smooth potentials or regular atomic lattices, imitating the honeycomb-structure of graphene. We implement walls of different hydroaffinity, different lattice constant, and different types of interaction with the water molecules. We find that in the hydrophobic regime the smooth wall generally represents a good abstraction of the atomically rough walls, while in the hydrophilic regime there are noticeable differences in structure and dynamics between all stages of wall roughness. For a small lattice constant however the smooth and the atomically rough wall still share a number of structural and dynamical similarities. Out of the three water models, TIP5P water shows the largest degree of tetrahedral ordering and is often the one that is least perturbed by the presence of the wall.
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Affiliation(s)
- Michael F Harrach
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Barbara Drossel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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69
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Zhou W, Wang YY, Lim TS, Pham T, Jain D, Burke PJ. Detection of single ion channel activity with carbon nanotubes. Sci Rep 2015; 5:9208. [PMID: 25778101 PMCID: PMC4361846 DOI: 10.1038/srep09208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/24/2015] [Indexed: 12/16/2022] Open
Abstract
Many processes in life are based on ion currents and membrane voltages controlled by a sophisticated and diverse family of membrane proteins (ion channels), which are comparable in size to the most advanced nanoelectronic components currently under development. Here we demonstrate an electrical assay of individual ion channel activity by measuring the dynamic opening and closing of the ion channel nanopores using single-walled carbon nanotubes (SWNTs). Two canonical dynamic ion channels (gramicidin A (gA) and alamethicin) and one static biological nanopore (α-hemolysin (α-HL)) were successfully incorporated into supported lipid bilayers (SLBs, an artificial cell membrane), which in turn were interfaced to the carbon nanotubes through a variety of polymer-cushion surface functionalization schemes. The ion channel current directly charges the quantum capacitance of a single nanotube in a network of purified semiconducting nanotubes. This work forms the foundation for a scalable, massively parallel architecture of 1d nanoelectronic devices interrogating electrophysiology at the single ion channel level.
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Affiliation(s)
- Weiwei Zhou
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
| | - Yung Yu Wang
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
| | - Tae-Sun Lim
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
| | - Ted Pham
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
| | - Dheeraj Jain
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
| | - Peter J. Burke
- Integrated Nanosystems Research Facility, Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA, 92697 USA
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70
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Seifert A, Göpfrich K, Burns JR, Fertig N, Keyser UF, Howorka S. Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS NANO 2015; 9:1117-26. [PMID: 25338165 PMCID: PMC4508203 DOI: 10.1021/nn5039433] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.
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Affiliation(s)
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jonathan R. Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Niels Fertig
- Nanion Technologies GmbH, D-80636 Munich, Germany
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- Address correspondence to ;
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Address correspondence to ;
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71
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Czekalska MA, Kaminski TS, Jakiela S, Tanuj Sapra K, Bayley H, Garstecki P. A droplet microfluidic system for sequential generation of lipid bilayers and transmembrane electrical recordings. LAB ON A CHIP 2015; 15:541-8. [PMID: 25412368 DOI: 10.1039/c4lc00985a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper demonstrates a microfluidic system that automates i) formation of a lipid bilayer at the interface between a pair of nanoliter-sized aqueous droplets in oil, ii) exchange of one droplet of the pair to form a new bilayer, and iii) current measurements on single proteins. A new microfluidic architecture is introduced - a set of traps designed to localize the droplets with respect to each other and with respect to the recording electrodes. The system allows for automated execution of experimental protocols by active control of the flow on chip with the use of simple external valves. Formation of stable artificial lipid bilayers, incorporation of α-hemolysin into the bilayers and electrical measurements of ionic transport through the protein pore are demonstrated.
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Affiliation(s)
- Magdalena A Czekalska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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72
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Harrach MF, Klameth F, Drossel B, Vogel M. Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water. J Chem Phys 2015; 142:034703. [DOI: 10.1063/1.4905557] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael F. Harrach
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Felix Klameth
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Barbara Drossel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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73
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del Rio Martinez JM, Zaitseva E, Petersen S, Baaken G, Behrends JC. Automated formation of lipid membrane microarrays for ionic single-molecule sensing with protein nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:119-125. [PMID: 25115837 DOI: 10.1002/smll.201402016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Efficient use of membrane protein nanopores in ionic single-molecule sensing requires technology for the reliable formation of suspended molecular membranes densely arrayed in formats that allow high-resolution electrical recording. Here, automated formation of bimolecular lipid layers is shown using a simple process where a poly(tetrafluoroethylene)-coated magnetic bar is remotely actuated to perform a turning motion, thereby spreading phospholipid in organic solvent on a nonpolar surface containing a <1 mm(2) 4 × 4 array of apertures with embedded microelectrodes (microelectrode cavity array). Parallel and high-resolution single-molecule detection by single nanopores is demonstrated on the resulting bilayer arrays, which are shown to form by a classical but very rapid self-assembly process. The technique provides a robust and scalable solution for the problem of reliable, automated formation of multiple independent lipid bilayers in a dense microarray format, while preserving the favorable electrical properties of the microelectrode cavity array.
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Affiliation(s)
- Juan M del Rio Martinez
- Laboratory for Membrane Physiology and -Technology, Department of Physiology, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
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74
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Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
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Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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75
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Gu Z, Ying YL, Cao C, He P, Long YT. Accurate Data Process for Nanopore Analysis. Anal Chem 2015; 87:907-13. [DOI: 10.1021/ac5028758] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zhen Gu
- Key
Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
- Department
of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
| | - Yi-Lun Ying
- Key
Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Chan Cao
- Key
Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Pingang He
- Department
of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
| | - Yi-Tao Long
- Key
Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
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76
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Chavis AE, Brady KT, Kothalawala N, Reiner JE. Voltage and blockade state optimization of cluster-enhanced nanopore spectrometry. Analyst 2015; 140:7718-25. [DOI: 10.1039/c5an01368b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cluster-enhanced nanopore spectrometry improves discrimination between different sized PEG molecules. This effect is analyzed as a function of the voltage and magnitude of the cluster blockade.
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Affiliation(s)
- Amy E. Chavis
- Department of Physics
- Virginia Commonwealth University
- Richmond
- USA
| | - Kyle T. Brady
- Department of Physics
- Virginia Commonwealth University
- Richmond
- USA
| | - Nuwan Kothalawala
- Department of Chemistry and Biochemistry
- University of Mississippi
- University
- USA
| | - Joseph E. Reiner
- Department of Physics
- Virginia Commonwealth University
- Richmond
- USA
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77
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Saha SC, Powl AM, Wallace BA, de Planque MRR, Morgan H. Screening ion-channel ligand interactions with passive pumping in a microfluidic bilayer lipid membrane chip. BIOMICROFLUIDICS 2015; 9:014103. [PMID: 25610515 PMCID: PMC4288537 DOI: 10.1063/1.4905313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 12/19/2014] [Indexed: 05/16/2023]
Abstract
We describe a scalable artificial bilayer lipid membrane platform for rapid electrophysiological screening of ion channels and transporters. A passive pumping method is used to flow microliter volumes of ligand solution across a suspended bilayer within a microfluidic chip. Bilayers are stable at flow rates up to ∼0.5 μl/min. Phospholipid bilayers are formed across a photolithographically defined aperture made in a dry film resist within the microfluidic chip. Bilayers are stable for many days and the low shunt capacitance of the thin film support gives low-noise high-quality single ion channel recording. Dose-dependent transient blocking of α-hemolysin with β-cyclodextrin (β-CD) and polyethylene glycol is demonstrated and dose-dependent blocking studies of the KcsA potassium channel with tetraethylammonium show the potential for determining IC50 values. The assays are fast (30 min for a complete IC50 curve) and simple and require very small amounts of compounds (100 μg in 15 μl). The technology can be scaled so that multiple bilayers can be addressed, providing a screening platform for ion channels, transporters, and nanopores.
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Affiliation(s)
- Shimul C Saha
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - Maurits R R de Planque
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Hywel Morgan
- Electronics and Computer Science and Institute for Life Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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78
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Weichbrodt C, Bajaj H, Baaken G, Wang J, Guinot S, Kreir M, Behrends JC, Winterhalter M, Fertig N. Antibiotic translocation through porins studied in planar lipid bilayers using parallel platforms. Analyst 2015; 140:4874-81. [DOI: 10.1039/c4an02335h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A comparative study of three different techniques Orbit16, Port-a-Patch and BLM applied for the investigation of antibiotic translocation.
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Affiliation(s)
| | | | | | - Jiajun Wang
- Nanion Technologies GmbH
- 80 636 Munich
- Germany
- Jacobs University Bremen
- 28 759 Bremen
| | | | | | - Jan C. Behrends
- Ionera Technologies GmbH
- 79104 Freiburg
- Germany
- Laboratory for Membrane Physiology and Technology
- Department of Physiology
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79
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Shi X, Gao R, Ying YL, Si W, Chen Y, Long YT. An integrated system for optical and electrical detection of single molecules/particles inside a solid-state nanopore. Faraday Discuss 2015; 184:85-99. [DOI: 10.1039/c5fd00060b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nanopore techniques have proven to be useful tools for single-molecule detection. The combination of optical detection and ionic current measurements enables a new possibility for the parallel readout of multiple nanopores without complex nanofluidics and embedded electrodes. In this study, we developed a new integrated system for the label-free optical and electrical detection of single molecules based on a metal-coated nanopore. The entire system, containing a dark-field microscopy system and an ultralow current detection system with high temporal resolution, was designed and fabricated. An Au-coated nanopore was used to generate the optical signal. Light scattering from a single Au-coated nanopore was measured under a dark-field microscope. A lab-built ultralow current detection system was designed for the correlated optical and electrical readout. This integrated system might provide more direct and detailed information on single analytes inside the nanopore compared with classical ionic current measurements.
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Affiliation(s)
- Xin Shi
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- Southeast University
- Nanjing 210096
- P. R. China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- Southeast University
- Nanjing 210096
- P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials
- Department of Chemistry
- East China University of Science and Technology
- Shanghai
- P. R. China
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80
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Piguet F, Discala F, Breton MF, Pelta J, Bacri L, Oukhaled A. Electroosmosis through α-Hemolysin That Depends on Alkali Cation Type. J Phys Chem Lett 2014; 5:4362-4367. [PMID: 26273988 DOI: 10.1021/jz502360c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We demonstrate experimentally the existence of an electroosmotic flow (EOF) through the wild-type nanopore of α-hemolysin in a large range of applied voltages and salt concentrations for two different salts, LiCl and KCl. EOF controls the entry frequency and residence time of small neutral molecules (β-cyclodextrins, βCD) in the nanopore. The strength of EOF depends on the applied voltage, on the salt concentration, and, interestingly, on the nature of the cations in solution. In particular, EOF is stronger in the presence of LiCl than KCl. We interpret our results with a simple theoretical model that takes into account the pore selectivity and the solvation of ions. A stronger EOF in the presence of LiCl is found to originate essentially in a stronger anionic selectivity of the pore. Our work provides a new and easy way to control EOF in protein nanopores, without resorting to chemical modifications of the pore.
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Affiliation(s)
- Fabien Piguet
- †LAMBE UMR 8587 CNRS, Cergy University, 33 Boulevard du Port, 95000 Cergy-Pontoise, France
| | - Francoise Discala
- †LAMBE UMR 8587 CNRS, Cergy University, 33 Boulevard du Port, 95000 Cergy-Pontoise, France
| | - Marie-France Breton
- †LAMBE UMR 8587 CNRS, Cergy University, 33 Boulevard du Port, 95000 Cergy-Pontoise, France
| | - Juan Pelta
- ‡LAMBE UMR 8587 CNRS, Évry University, Boulevard François Mitterrand, 91000 Évry, France
| | - Laurent Bacri
- ‡LAMBE UMR 8587 CNRS, Évry University, Boulevard François Mitterrand, 91000 Évry, France
| | - Abdelghani Oukhaled
- †LAMBE UMR 8587 CNRS, Cergy University, 33 Boulevard du Port, 95000 Cergy-Pontoise, France
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81
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Pastoriza-Gallego M, Breton MF, Discala F, Auvray L, Betton JM, Pelta J. Evidence of unfolded protein translocation through a protein nanopore. ACS NANO 2014; 8:11350-11360. [PMID: 25380310 DOI: 10.1021/nn5042398] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein nanopores are mainly used to study transport, unfolding, intrinsically disordered proteins, protein-pore interactions, and protein-ligand complexes. This single-molecule sensor for biomedical and biotechnological applications is promising but until now direct proof of protein translocation through a narrow channel is lacking. Here, we report the translocation of a chimera molecule through the aerolysin nanopore in the presence of a denaturing agent, guanidium chloride (1.5 M) and KCl (1 M). The chimera molecule is composed of the recombinant MalE protein with a unique cysteine residue at the C-terminal position covalently linked to a single-stranded DNA oligonucleotide. Real-time polymerase chain reaction (PCR) was used to detect the presence of chimera molecules that have been effectively translocated from the cis to trans chamber of the set up. Comparing the electrical signature of the chimera related to the protein or oligonucleotide alone demonstrates that each type of molecule displays different dynamics in term of transport time, event frequency, and current blockade. This original approach provides the possibility to study protein translocation through different biological, artificial, and biomimetic nanopores or nanotubes. New future applications are now conceivable such as protein refolding at the nanopore exit, peptides and protein sequencing, and peptide characterization for diagnostics.
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Affiliation(s)
- Manuela Pastoriza-Gallego
- CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise , 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
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82
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Angevine CE, Chavis AE, Kothalawala N, Dass A, Reiner JE. Enhanced Single Molecule Mass Spectrometry via Charged Metallic Clusters. Anal Chem 2014; 86:11077-85. [DOI: 10.1021/ac503425g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christopher E. Angevine
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Amy E. Chavis
- 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 E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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83
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Ivankin A, Henley RY, Larkin J, Carson S, Toscano ML, Wanunu M. Label-free optical detection of biomolecular translocation through nanopore arrays. ACS NANO 2014; 8:10774-81. [PMID: 25232895 PMCID: PMC4212781 DOI: 10.1021/nn504551d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.
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Affiliation(s)
- Andrey Ivankin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael L. Toscano
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Address correspondence to
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84
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Abstract
Artificial lipid bilayers have many uses. They are well established for scientific studies of reconstituted ion channels, used to host engineered pore proteins for sensing, and can potentially be applied in DNA sequencing. Droplet bilayers have significant technological potential for enabling many of these applications due to their compatibility with automation and array platforms. To further develop this potential, we have simplified the formation and electrical measurement of droplet bilayers using an apparatus that only requires fluid dispensation. We achieved simultaneous bilayer formation and measurement over a 32-element array with ~80% yield and no operator input following fluid addition. Cycling these arrays resulted in the formation and measurement of 96 out of 120 possible bilayers in 80 minutes, a sustainable rate that could significantly increase with automation and greater parallelization. This turn-key, high-yield approach to making artificial lipid bilayers requires no training, making the capability of creating and measuring lipid bilayers and ion channels accessible to a much wider audience. In addition, this approach is low-cost, parallelizable, and automatable, allowing high-throughput studies of ion channels and pore proteins in lipid bilayers for sensing or screening applications.
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85
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Mutlu H, Lutz JF. Reading Polymers: Sequencing of Natural and Synthetic Macromolecules. Angew Chem Int Ed Engl 2014; 53:13010-9. [DOI: 10.1002/anie.201406766] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/24/2014] [Indexed: 11/07/2022]
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86
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Mutlu H, Lutz JF. “Lesen” von Polymeren: Die Sequenzierung natürlicher und synthetischer Makromoleküle. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406766] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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87
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Jeon BJ, Muthukumar M. Determination of Molecular Weights in Polyelectrolyte Mixtures Using Polymer Translocation through a Protein Nanopore. ACS Macro Lett 2014; 3:911-915. [PMID: 25243100 PMCID: PMC4165535 DOI: 10.1021/mz500404e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/01/2014] [Indexed: 11/28/2022]
Abstract
We introduce a single molecular analysis technique for the evaluation of molecular weight distributions of polyelectrolyte solutions by measuring translocation times of sodium polystyrenesulfonate (NaPSS) chains in a mixture passing through an α-hemolysin protein nanopore. The ionic current through an α-hemolysin nanopore is partially blocked transiently when the pore is occupied by a polymer chain with an average residence time proportional to the molecular weight of the polymer chain. We have measured the translocation times for an equimolar mixture of four different molecular weight NaPSS standards and observed distinct translocation time distribution peaks, each of which corresponding to the different components in the mixture. Size exclusion chromatography analyses were performed on the equimolar and equiweight NaPSS mixtures of the same components and compared with the translocation time measurements. The experimental results demonstrate that measuring translocation times can be a competitive technique for estimating the broad molecular weight distributions of polyelectrolytes.
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Affiliation(s)
- Byoung-jin Jeon
- Department of Polymer Science
and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Murugappan Muthukumar
- Department of Polymer Science
and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
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88
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Cabello-Aguilar S, Abou Chaaya A, Picaud F, Bechelany M, Pochat-Bohatier C, Yesylevskyy S, Kraszewski S, Bechelany MC, Rossignol F, Balanzat E, Janot JM, Miele P, Dejardin P, Balme S. Experimental and simulation studies of unusual current blockade induced by translocation of small oxidized PEG through a single nanopore. Phys Chem Chem Phys 2014; 16:17883-92. [DOI: 10.1039/c4cp01954g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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89
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90
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91
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Howorka S, Hesse J. Microarrays and single molecules: an exciting combination. SOFT MATTER 2014; 10:931-41. [PMID: 24651891 DOI: 10.1039/c3sm52561a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H 0AJ, UK.
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92
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Tsuji Y, Kawano R, Osaki T, Kamiya K, Miki N, Takeuchi S. Droplet Split-and-Contact Method for High-Throughput Transmembrane Electrical Recording. Anal Chem 2013; 85:10913-9. [DOI: 10.1021/ac402299z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yutaro Tsuji
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
- Department
of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama 223-8522, Japan
| | - Ryuji Kawano
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
| | - Koki Kamiya
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
| | - Norihisa Miki
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
- Department
of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama 223-8522, Japan
| | - Shoji Takeuchi
- Artificial
Cell
Membrane System Group, Kanagawa Academy of Science and Technology (KAST), 3-2-1
Sakado, Takatsu-ku, Kawasaki 213-0012, Japan
- CIRMM-IIS, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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93
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Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc Natl Acad Sci U S A 2013; 110:E4417-26. [PMID: 24194548 DOI: 10.1073/pnas.1312739110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In stochastic sensing, the association and dissociation of analyte molecules is observed as the modulation of an ionic current flowing through a single engineered protein pore, enabling the label-free determination of rate and equilibrium constants with respect to a specific binding site. We engineered sensors based on the staphylococcal α-hemolysin pore to allow the single-molecule detection and characterization of protein kinase-peptide interactions. We enhanced this approach by using site-specific proteolysis to generate pores bearing a single peptide sensor element attached by an N-terminal peptide bond to the trans mouth of the pore. Kinetics and affinities for the Pim protein kinases (Pim-1, Pim-2, and Pim-3) and cAMP-dependent protein kinase were measured and found to be independent of membrane potential and in good agreement with previously reported data. Kinase binding exhibited a distinct current noise behavior that forms a basis for analyte discrimination. Finally, we observed unusually high association rate constants for the interaction of Pim kinases with their consensus substrate Pimtide (~10(7) to 10(8) M(-1) · s(-1)), the result of electrostatic enhancement, and propose a cellular role for this phenomenon.
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94
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Kang I, Wang Y, Reagan C, Fu Y, Wang MX, Gu LQ. Designing DNA interstrand lock for locus-specific methylation detection in a nanopore. Sci Rep 2013; 3:2381. [PMID: 24135881 PMCID: PMC3798886 DOI: 10.1038/srep02381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/12/2013] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is an important epigenetic regulation of gene transcription. Locus-specific DNA methylation can be used as biomarkers in various diseases including cancer. Many methods have been developed for genome-wide methylation analysis, but molecular diagnotics needs simple tools to determine methylation states at individual CpG sites in a gene fragment. In this report, we utilized the nanopore single-molecule sensor to investigate a base-pair specific metal ion/nucleic acids interaction, and explored its potential application in locus-specific DNA methylation analysis. We identified that divalent Mercury ion (Hg2+) can selectively bind a uracil-thymine mismatch (U-T) in a dsDNA. The Hg2+ binding creates a reversible interstrand lock, called MercuLock, which enhances the hybridization strength by two orders of magnitude. Such MercuLock cannot be formed in a 5-methylcytosine-thymine mismatch (mC-T). By nanopore detection of dsDNA stability, single bases of uracil and 5-methylcytosine can be distinguished. Since uracil is converted from cytosine by bisulfite treatment, cytosine and 5′-methylcytosine can be discriminated. We have demonstrated the methylation analysis of multiple CpGs in a p16 gene CpG island. This single-molecule assay may have potential in detection of epigenetic cancer biomarkers in biofluids, with an ultimate goal for early diagnosis of cancer.
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Affiliation(s)
- Insoon Kang
- Department of Bioengineering and Dalton Cardiovascular Research Center
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95
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Kawano R, Tsuji Y, Sato K, Osaki T, Kamiya K, Hirano M, Ide T, Miki N, Takeuchi S. Automated parallel recordings of topologically identified single ion channels. Sci Rep 2013; 3:1995. [PMID: 23771282 PMCID: PMC3683667 DOI: 10.1038/srep01995] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/30/2013] [Indexed: 02/07/2023] Open
Abstract
Although ion channels are attractive targets for drug discovery, the systematic screening of ion channel-targeted drugs remains challenging. To facilitate automated single ion-channel recordings for the analysis of drug interactions with the intra- and extracellular domain, we have developed a parallel recording methodology using artificial cell membranes. The use of stable lipid bilayer formation in droplet chamber arrays facilitated automated, parallel, single-channel recording from reconstituted native and mutated ion channels. Using this system, several types of ion channels, including mutated forms, were characterised by determining the protein orientation. In addition, we provide evidence that both intra- and extracellular amyloid-beta fragments directly inhibit the channel open probability of the hBK channel. This automated methodology provides a high-throughput drug screening system for the targeting of ion channels and a data-intensive analysis technique for studying ion channel gating mechanisms.
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Affiliation(s)
- Ryuji Kawano
- BioMicrosystems Project, Kanagawa Academy of Science and Technology (KAST), Kawasaki, Japan
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96
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Panja D, Barkema GT, Kolomeisky AB. Through the eye of the needle: recent advances in understanding biopolymer translocation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:413101. [PMID: 24025200 DOI: 10.1088/0953-8984/25/41/413101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics during the motion through channels with unprecedented spatial and temporal resolution. These striking experimental studies have stimulated many theoretical developments. In this short theory-experiment review, we discuss recent progress in this field with a strong focus on non-equilibrium aspects of polymer dynamics during the translocation process.
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Affiliation(s)
- Debabrata Panja
- Institute for Theoretical Physics, Universiteit Utrecht, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands. Institute for Theoretical Physics, Universiteit van Amsterdam, Science Park 904, Postbus 94485, 1090 GL Amsterdam, The Netherlands
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97
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Fennouri A, Daniel R, Pastoriza-Gallego M, Auvray L, Pelta J, Bacri L. Kinetics of Enzymatic Degradation of High Molecular Weight Polysaccharides through a Nanopore: Experiments and Data-Modeling. Anal Chem 2013; 85:8488-92. [DOI: 10.1021/ac4020929] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aziz Fennouri
- Université d’Évry Val d’Essonne, Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, F-91025 Evry, France
- CNRS UMR 8587,
Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, F-91025 Evry, France
| | - Régis Daniel
- CNRS UMR 8587,
Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, F-91025 Evry, France
| | - Manuela Pastoriza-Gallego
- Université de Cergy-Pontoise, Laboratoire Analyse et Modélisation
pour la Biologie et l’Environnement, F-95302 Cergy-Pontoise, France
| | - Loïc Auvray
- CNRS UMR
7057,
Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, F-75205 Paris, France
| | - Juan Pelta
- Université d’Évry Val d’Essonne, Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, F-91025 Evry, France
| | - Laurent Bacri
- Université d’Évry Val d’Essonne, Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, F-91025 Evry, France
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98
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Rosenstein JK, Ramakrishnan S, Roseman J, Shepard KL. Single ion channel recordings with CMOS-anchored lipid membranes. NANO LETTERS 2013; 13:2682-6. [PMID: 23634707 PMCID: PMC3683112 DOI: 10.1021/nl400822r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We present single-ion-channel recordings performed with biomimetic lipid membranes which are directly attached to the surface of a complementary metal-oxide-semiconductor (CMOS) preamplifier chip. With this system we resolve single-channel currents from several types of bacterial ion channels, including fluctuations of a single alamethicin channel at a bandwidth of 1 MHz which represent the fastest single-ion-channel recordings reported to date. The platform is also used for high-resolution α-hemolysin nanopore recordings. These results illustrate the high signal fidelity, fine temporal resolution, small geometry, and multiplexed integration which can be achieved by leveraging integrated semiconductor platforms for advanced ion channel interfaces.
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Affiliation(s)
- Jacob K Rosenstein
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA.
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99
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Bell NAW, Thacker VV, Hernández-Ainsa S, Fuentes-Perez ME, Moreno-Herrero F, Liedl T, Keyser UF. Multiplexed ionic current sensing with glass nanopores. LAB ON A CHIP 2013; 13:1859-62. [PMID: 23563625 DOI: 10.1039/c3lc50069a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report a method for simultaneous ionic current measurements of single molecules across up to 16 solid state nanopore channels. Each device, costing less than $20, contains 16 glass nanopores made by laser assisted capillary pulling. We demonstrate simultaneous multichannel detection of double stranded DNA and trapping of DNA origami nanostructures to form hybrid nanopores.
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100
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Stimberg VC, Bomer JG, van Uitert I, van den Berg A, Le Gac S. High yield, reproducible and quasi-automated bilayer formation in a microfluidic format. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1076-1085. [PMID: 23139010 DOI: 10.1002/smll.201201821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/27/2012] [Indexed: 05/28/2023]
Abstract
A microfluidic platform is reported for various experimentation schemes on cell membrane models and membrane proteins using a combination of electrical and optical measurements, including confocal microscopy. Bilayer lipid membranes (BLMs) are prepared in the device upon spontaneous and instantaneous thinning of the lipid solution in a 100-μm dry-etched aperture in a 12.5-μm thick Teflon foil. Using this quasi-automated approach, a remarkable 100% membrane formation yield is reached (including reflushing in 4% of the cases), and BLMs are stable for up to 36 h. Furthermore, the potential of this platform is demonstrated for (i) the in-depth characterization of BLMs comprising both synthetic and natural lipids (1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) and L-α-phosphatidylcholine (L-α-PC)/cholesterol, respectively) in terms of seal resistance, capacitance, surface area, specific capacitance, and membrane hydrophobic thickness; (ii) confocal microscopy imaging of phase separation in sphingomyelin/L-α-PC/cholesterol ternary membranes; (iii) electrical measurements of individual nanopores (α-hemolysin, gramicidin); and (iv) indirect assessment of the alteration of membrane properties upon exposure to chemical stimuli using the natural nanopore gramicidin as a sensor.
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Affiliation(s)
- Verena C Stimberg
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
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