1
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Cingolani G, Lokareddy R, Hou CF, Forti F, Iglesias S, Li F, Pavlenok M, Niederweis M, Briani F. Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor. RESEARCH SQUARE 2024:rs.3.rs-3941185. [PMID: 38463957 PMCID: PMC10925440 DOI: 10.21203/rs.3.rs-3941185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DEV is an obligatory lytic Pseudomonas phage of the N4-like genus, recently reclassified as Schitoviridae. The DEV genome encodes 91 ORFs, including a 3,398 amino acid virion-associated RNA polymerase. Here, we describe the complete architecture of DEV, determined using a combination of cryo-electron microscopy localized reconstruction, biochemical methods, and genetic knockouts. We built de novo structures of all capsid factors and tail components involved in host attachment. We demonstrate that DEV long tail fibers are essential for infection of Pseudomonas aeruginosa and dispensable for infecting mutants with a truncated lipopolysaccharide devoid of the O-antigen. We identified DEV ejection proteins and, unexpectedly, found that the giant DEV RNA polymerase, the hallmark of the Schitoviridae family, is an ejection protein. We propose that DEV ejection proteins form a genome ejection motor across the host cell envelope and that these structural principles are conserved in all Schitoviridae.
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2
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Mimura H, Osaki T, Takamori S, Nakao K, Takeuchi S. Lipid Bilayer Reformation Using the Wiping Blade for Improved Ion Channel Analysis. Anal Chem 2023; 95:17354-17361. [PMID: 37968939 DOI: 10.1021/acs.analchem.3c03707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The measurement of ion permeation activity across planar lipid bilayers is a useful technique for the functional analysis and drug evaluation of ion channels at the single-molecule level. To enhance the data throughput, parallelization of lipid bilayers is desirable. However, existing parallelized approaches face challenges in simultaneously and efficiently measuring ion channel activities under various conditions on one chip. In this study, we propose an approach to overcome these limitations by developing a device capable of repeated measurements of ion channels incorporated into individually arrayed lipid bilayers. Our device forms an array of a lipid bilayer at a micropore on a separator by merging two lipid monolayers assembled on the surface of aqueous droplets. We introduce a vertically moving, blade-shaped module─referred to as a "wiping blade"─which enables controlled disruption and reformation of the bilayer at the micropore. By optimizing the surface properties and clearance of the wiping blade, we successfully achieved repeated bilayer formation. The arrayed lipid bilayer device with the integrated wiping blade module demonstrates a 5-fold improvement in data throughput during ion channel activity measurements. Finally, we validate the practical utility of our device by evaluating the effects of an ion channel inhibitor. The developed device opens new avenues for high-throughput analysis and screening of ion channels, leading to significant advancements in drug discovery and functional studies of membrane proteins. It offers a powerful tool for researchers in the field and holds promise for accelerating drug development by targeting ion channels.
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Affiliation(s)
- Hisatoshi Mimura
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Toshihisa Osaki
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
- MAQsys Inc., 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Sho Takamori
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Kenji Nakao
- MAQsys Inc., 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Shoji Takeuchi
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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3
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Protein identification using a digestion-free nanopore approach. Nat Biotechnol 2023; 41:1078-1079. [PMID: 36624152 DOI: 10.1038/s41587-022-01599-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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4
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Yu L, Kang X, Li F, Mehrafrooz B, Makhamreh A, Fallahi A, Foster JC, Aksimentiev A, Chen M, Wanunu M. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol 2023; 41:1130-1139. [PMID: 36624148 PMCID: PMC10329728 DOI: 10.1038/s41587-022-01598-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/02/2022] [Indexed: 01/10/2023]
Abstract
The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is ~1.4 nm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.
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Affiliation(s)
- Luning Yu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Fanjun Li
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Behzad Mehrafrooz
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Computational 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
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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5
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Chingarande RG, Tian K, Kuang Y, Sarangee A, Hou C, Ma E, Ren J, Hawkins S, Kim J, Adelstein R, Chen S, Gillis KD, Gu LQ. Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor. Proc Natl Acad Sci U S A 2023; 120:e2108118120. [PMID: 37276386 PMCID: PMC10268594 DOI: 10.1073/pnas.2108118120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.
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Affiliation(s)
- Rugare G. Chingarande
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Kai Tian
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Yu Kuang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Aby Sarangee
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Chengrui Hou
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Emily Ma
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Jarett Ren
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sam Hawkins
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Joshua Kim
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Ray Adelstein
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sally Chen
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Kevin D. Gillis
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Li-Qun Gu
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
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6
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Kang X, Wu C, Alibakhshi MA, Liu X, Yu L, Walt DR, Wanunu M. Nanopore-Based Fingerprint Immunoassay Based on Rolling Circle Amplification and DNA Fragmentation. ACS NANO 2023; 17:5412-5420. [PMID: 36877993 PMCID: PMC10629239 DOI: 10.1021/acsnano.2c09889] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
In recent years, nanopore-based sequencers have become robust tools with unique advantages for genomics applications. However, progress toward applying nanopores as highly sensitive, quantitative diagnostic tools has been impeded by several challenges. One major limitation is the insufficient sensitivity of nanopores in detecting disease biomarkers, which are typically present at pM or lower concentrations in biological fluids, while a second limitation is the general absence of unique nanopore signals for different analytes. To bridge this gap, we have developed a strategy for nanopore-based biomarker detection that utilizes immunocapture, isothermal rolling circle amplification, and sequence-specific fragmentation of the product to release multiple DNA reporter molecules for nanopore detection. These DNA fragment reporters produce sets of nanopore signals that form distinctive fingerprints, or clusters. This fingerprint signature therefore allows the identification and quantification of biomarker analytes. As a proof of concept, we quantify human epididymis protein 4 (HE4) at low pM levels in a few hours. Future improvement of this method by integration with a nanopore array and microfluidics-based chemistry can further reduce the limit of detection, allow multiplexed biomarker detection, and further reduce the footprint and cost of existing laboratory and point-of-care devices.
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Affiliation(s)
- Xinqi Kang
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Connie Wu
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School and Wyss Institute for Biologically Inspired
Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Mohammad Amin Alibakhshi
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Xingyan Liu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Luning Yu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School and Wyss Institute for Biologically Inspired
Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
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7
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Di Muccio G, Morozzo della Rocca B, Chinappi M. Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores. ACS NANO 2022; 16:8716-8728. [PMID: 35587777 PMCID: PMC9245180 DOI: 10.1021/acsnano.1c03017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.
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Affiliation(s)
- Giovanni Di Muccio
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
| | - Blasco Morozzo della Rocca
- Dipartimento
di Biologia, Università di Roma Tor
Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Mauro Chinappi
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
- E-mail:
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8
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Wang L, Wang H, Chen X, Zhou S, Wang Y, Guan X. Chemistry solutions to facilitate nanopore detection and analysis. Biosens Bioelectron 2022; 213:114448. [PMID: 35716643 DOI: 10.1016/j.bios.2022.114448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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9
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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10
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Ogishi K, Osaki T, Morimoto Y, Takeuchi S. 3D printed microfluidic devices for lipid bilayer recordings. LAB ON A CHIP 2022; 22:890-898. [PMID: 35133381 DOI: 10.1039/d1lc01077h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper verifies the single-step and monolithic fabrication of 3D structural lipid bilayer devices using stereolithography. Lipid bilayer devices are utilized to host membrane proteins in vitro for biological assays or sensing applications. There is a growing demand to fabricate functional lipid bilayer devices with a short lead-time, and the monolithic fabrication of components by 3D printing is highly anticipated. However, the prerequisites of 3D printing materials which lead to reproducible lipid bilayer formation are still unknown. Here, we examined the feasibility of membrane protein measurement using lipid bilayer devices fabricated by stereolithography. The 3D printing materials were characterized and the surface smoothness and hydrophobicity were found to be the relevant factors for successful lipid bilayer formation. The devices were comparable to the ones fabricated by conventional procedures in terms of measurement performances like the amplitude of noise and the waiting time for lipid bilayer formation. We further demonstrated the extendibility of the technology for the functionalization of devices, such as incorporating microfluidic channels for solution exchangeability and arraying multiple chambers for robust measurement.
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Affiliation(s)
- Kazuto Ogishi
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Toshihisa Osaki
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Yuya Morimoto
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Shoji Takeuchi
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
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11
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Control of subunit stoichiometry in single-chain MspA nanopores. Biophys J 2022; 121:742-754. [PMID: 35101416 PMCID: PMC8943699 DOI: 10.1016/j.bpj.2022.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/18/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Transmembrane protein channels enable fast and highly sensitive detection of single molecules. Nanopore sequencing of DNA was achieved using an engineered Mycobacterium smegmatis porin A (MspA) in combination with a motor enzyme. Due to its favorable channel geometry, the octameric MspA pore exhibits the highest current level compared with other pore proteins. To date, MspA is the only protein nanopore with a published record of DNA sequencing. While widely used in commercial devices, nanopore sequencing of DNA suffers from significant base-calling errors due to stochastic events of the complex DNA-motor-pore combination and the contribution of up to five nucleotides to the signal at each position. Different mutations in specific subunits of a pore protein offer an enormous potential to improve nucleotide resolution and sequencing accuracy. However, individual subunits of MspA and other oligomeric protein pores are randomly assembled in vivo and in vitro, preventing the efficient production of designed pores with different subunit mutations. In this study, we converted octameric MspA into a single-chain pore by connecting eight subunits using peptide linkers. Lipid bilayer experiments demonstrated that single-chain MspA formed membrane-spanning channels and discriminated all four nucleotides identical to MspA produced from monomers in DNA hairpin experiments. Single-chain constructs comprising three, five, six, and seven connected subunits assembled to functional channels, demonstrating a remarkable plasticity of MspA to different subunit stoichiometries. Thus, single-chain MspA constitutes a new milestone in the optimization of MspA as a biosensor for DNA sequencing and many other applications by enabling the production of pores with distinct subunit mutations and pore diameters.
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12
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Yao YC, Li Z, Gillen AJ, Yosinski S, Reed MA, Noy A. Electrostatic gating of ion transport in carbon nanotube porins: A modeling study. J Chem Phys 2021; 154:204704. [PMID: 34241182 DOI: 10.1063/5.0049550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Carbon nanotube porins (CNTPs) are biomimetic membrane channels that demonstrate excellent biocompatibility and unique water and ion transport properties. Gating transport in CNTPs with external voltage could increase control over ion flow and selectivity. Herein, we used continuum modeling to probe the parameters that enable and further affect CNTP gating efficiency, including the size and composition of the supporting lipid membrane, slip flow in the carbon nanotube, and the intrinsic electronic properties of the nanotube. Our results show that the optimal gated CNTP device consists of a semiconducting CNTP inserted into a small membrane patch containing an internally conductive layer. Moreover, we demonstrate that the ionic transport modulated by gate voltages is controlled by the charge distribution along the CNTP under the external gate electric potential. The theoretical understanding developed in this study offers valuable guidance for the design of gated CNTP devices for nanofluidic studies, novel biomimetic membranes, and cellular interfaces in the future.
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Affiliation(s)
- Yun-Chiao Yao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Zhongwu Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Alice J Gillen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Shari Yosinski
- Department of Electrical Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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13
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Fujinami Tanimoto IM, Cressiot B, Jarroux N, Roman J, Patriarche G, Le Pioufle B, Pelta J, Bacri L. Selective target protein detection using a decorated nanopore into a microfluidic device. Biosens Bioelectron 2021; 183:113195. [PMID: 33857755 DOI: 10.1016/j.bios.2021.113195] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
Solid-state nanopores provide a powerful tool to electrically analyze nanoparticles and biomolecules at single-molecule resolution. These biosensors need to have a controlled surface to provide information about the analyte. Specific detection remains limited due to nonspecific interactions between the molecules and the nanopore. Here, a polymer surface modification to passivate the membrane is performed. This functionalization improves nanopore stability and ionic conduction. Moreover, one can control the nanopore diameter and the specific interactions between protein and pore surface. The effect of ionic strength and pH are probed. Which enables control of the electroosmotic driving force and dynamics. Furthermore, a study of polymer chain structure and permeability in the pore are carried out. The nanopore chip is integrated into a microfluidic device to ease its handling. Finally, a discussion of an ionic conductance model through a permeable crown along the nanopore surface is elucidated. The proof of concept is demonstrated by the capture of free streptavidin by the biotins grafted into the nanopore. In the future, this approach could be used for virus diagnostic, nanoparticle or biomarker sensing.
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Affiliation(s)
- Izadora Mayumi Fujinami Tanimoto
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France; Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France
| | | | - Nathalie Jarroux
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
| | - Jean Roman
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France
| | - Gilles Patriarche
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - Bruno Le Pioufle
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France.
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France.
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France.
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14
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Sun K, Chen P, Yan S, Yuan W, Wang Y, Li X, Dou L, Zhao C, Zhang J, Wang Q, Fu Z, Wei L, Xin Z, Tang Z, Yan Y, Peng Y, Ying B, Chen J, Geng J. Ultrasensitive Nanopore Sensing of Mucin 1 and Circulating Tumor Cells in Whole Blood of Breast Cancer Patients by Analyte-Triggered Triplex-DNA Release. ACS APPLIED MATERIALS & INTERFACES 2021; 13:21030-21039. [PMID: 33905228 DOI: 10.1021/acsami.1c03538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The characterization of circulating tumor cells (CTCs) by liquid biopsy has a great potential for precision medicine in oncology. Here, a universal and tandem logic-based strategy is developed by combining multiple nanomaterials and nanopore sensing for the determination of mucin 1 protein (MUC1) and breast cancer CTCs in real samples. The strategy consists of analyte-triggered signal conversion, cascaded amplification via nanomaterials including copper sulfide nanoparticles (CuS NPs), silver nanoparticles (Ag NPs), and biomaterials including DNA hydrogel and DNAzyme, and single-molecule-level detection by nanopore sensing. The amplification of the non-DNA nanomaterial gives this method considerable stability, significantly lowers the limit of detection (LOD), and enhances the anti-interference performance for complicated samples. As a result, the ultrasensitive detection of MUC1 could be achieved in the range of 0.0005-0.5 pg/mL, with an LOD of 0.1 fg/mL. Moreover, we further tested MUC1 as a biomarker for the clinical diagnosis of breast cancer CTCs under double-blind conditions on the basis of this strategy, and MCF-7 cells could be accurately detected in the range from 5 to 2000 cells/mL, with an LOD of 2 cells/mL within 6 h. The detection results of the 19 clinical samples were highly consistent with those of the clinical pathological sections, nuclear magnetic resonance imaging, and color ultrasound. These results demonstrate the validity and reliability of our method and further proved the feasibility of MUC1 as a clinical diagnostic biomarker for CTCs.
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Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Linqin Dou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jianfu Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Qiang Wang
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhoukai Fu
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Long Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhaodan Xin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhuoyun Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yiman Peng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jie Chen
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
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15
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Electrical unfolding of cytochrome c during translocation through a nanopore constriction. Proc Natl Acad Sci U S A 2021; 118:2016262118. [PMID: 33883276 DOI: 10.1073/pnas.2016262118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiNx) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of ∼30 to 100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field-induced deformability.
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16
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Yu L, Kang X, Alibakhshi MA, Pavlenok M, Niederweis M, Wanunu M. Stable polymer bilayers for protein channel recordings at high guanidinium chloride concentrations. Biophys J 2021; 120:1537-1541. [PMID: 33617833 DOI: 10.1016/j.bpj.2021.02.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 11/28/2022] Open
Abstract
The use of chaotropic reagents is common in biophysical characterization of biomolecules. When the study involves transmembrane protein channels, the stability of the protein channel and supporting bilayer membrane must be considered. In this letter, we show that planar bilayers composed of poly(1,2-butadiene)-b-poly(ethylene oxide) diblock copolymer are stable and leak-free at high guanidinium chloride concentrations, in contrast to diphytanoyl phosphatidylcholine bilayers, which exhibit deleterious leakage under similar conditions. Furthermore, insertion and functional analysis of channels such as α-hemolysin and MspA are straightforward in these polymer membranes. Finally, we demonstrate that α-hemolysin channels maintain their structural integrity at 2 M guanidinium chloride concentrations using blunt DNA hairpins as molecular reporters.
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Affiliation(s)
| | | | | | - Mikhail Pavlenok
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Meni Wanunu
- Department of Physics; Department of Bioengineering; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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17
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Parallel Recordings of Transmembrane hERG Channel Currents Based on Solvent-Free Lipid Bilayer Microarray. MICROMACHINES 2021; 12:mi12010098. [PMID: 33478052 PMCID: PMC7835820 DOI: 10.3390/mi12010098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/23/2022]
Abstract
The reconstitution of ion-channel proteins in artificially formed bilayer lipid membranes (BLMs) forms a well-defined system for the functional analysis of ion channels and screening of the effects of drugs that act on these proteins. To improve the efficiency of the BLM reconstitution system, we report on a microarray of stable solvent-free BLMs formed in microfabricated silicon (Si) chips, where micro-apertures with well-defined nano- and micro-tapered edges were fabricated. Sixteen micro-wells were manufactured in a chamber made of Teflon®, and the Si chips were individually embedded in the respective wells as a recording site. Typically, 11 to 16 BLMs were simultaneously formed with an average BLM number of 13.1, which corresponded to a formation probability of 82%. Parallel recordings of ion-channel activities from multiple BLMs were successfully demonstrated using the human ether-a-go-go-related gene (hERG) potassium channel, of which the relation to arrhythmic side effects following drug treatment is well recognized.
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18
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Ito Y, Osaki T, Kamiya K, Yamada T, Miki N, Takeuchi S. Rapid and Resilient Detection of Toxin Pore Formation Using a Lipid Bilayer Array. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2005550. [PMID: 33191570 DOI: 10.1002/smll.202005550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/14/2020] [Indexed: 06/11/2023]
Abstract
An artificial cell membrane is applied to study the pore formation mechanisms of bacterial pore-forming toxins for therapeutic applications. Electrical monitoring of ionic current across the membrane provides information on the pore formation process of toxins at the single pore level, as well as the pore characteristics such as dimensions and ionic selectivity. However, the efficiency of pore formation detection largely depends on the encounter probability of toxin to the membrane and the fragility of the membrane. This study presents a bilayer lipid membrane array that parallelizes 4 or 16 sets of sensing elements composed of pairs of a membrane and a series electrical resistor. The series resistor prevents current overflow attributed to membrane rupture, and enables current monitoring of the parallelized membranes with a single detector. The array system shortens detection time of a pore-forming protein and improves temporal stability. The current signature represents the states of pore formation and rupture at respective membranes. The developed system will help in understanding the toxic activity of pore-forming toxins.
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Affiliation(s)
- Yoshihisa Ito
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Center for Multidisciplinary and Design Science, School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Koki Kamiya
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Tetsuya Yamada
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Norihisa Miki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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