1
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Punia B, Chaudhury S. Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity. J Phys Chem B 2024; 128:1876-1883. [PMID: 38355410 DOI: 10.1021/acs.jpcb.3c08350] [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: 02/16/2024]
Abstract
Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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2
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Rostovtseva TK, Weinrich M, Jacobs D, Rosencrans WM, Bezrukov SM. Dimeric Tubulin Modifies Mechanical Properties of Lipid Bilayer, as Probed Using Gramicidin A Channel. Int J Mol Sci 2024; 25:2204. [PMID: 38396879 PMCID: PMC10889239 DOI: 10.3390/ijms25042204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Using the gramicidin A channel as a molecular probe, we show that tubulin binding to planar lipid membranes changes the channel kinetics-seen as an increase in the lifetime of the channel dimer-and thus points towards modification of the membrane's mechanical properties. The effect is more pronounced in the presence of non-lamellar lipids in the lipid mixture used for membrane formation. To interpret these findings, we propose that tubulin binding redistributes the lateral pressure of lipid packing along the membrane depth, making it closer to the profile expected for lamellar lipids. This redistribution happens because tubulin perturbs the lipid headgroup spacing to reach the membrane's hydrophobic core via its amphiphilic α-helical domain. Specifically, it increases the forces of repulsion between the lipid headgroups and reduces such forces in the hydrophobic region. We suggest that the effect is reciprocal, meaning that alterations in lipid bilayer mechanics caused by membrane remodeling during cell proliferation in disease and development may also modulate tubulin membrane binding, thus exerting regulatory functions. One of those functions includes the regulation of protein-protein interactions at the membrane surface, as exemplified by VDAC complexation with tubulin.
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Affiliation(s)
- Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
| | - Michael Weinrich
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Daniel Jacobs
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
| | - William M. Rosencrans
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA (S.M.B.)
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3
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Aguilella-Arzo M, Hoogerheide DP, Doucet M, Wang H, Aguilella VM. Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure. J Am Chem Soc 2024; 146:2701-2710. [PMID: 38291994 PMCID: PMC10835712 DOI: 10.1021/jacs.3c12348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/01/2024]
Abstract
Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein-protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.
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Affiliation(s)
- Marcel Aguilella-Arzo
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071, Castellón, Spain
| | - David P. Hoogerheide
- Center
for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Mathieu Doucet
- Neutron
Scattering Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hanyu Wang
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Vicente M. Aguilella
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071, Castellón, Spain
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4
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Zhang A, Guo Z, Ge G, Liu Z. Insights into In Vivo Environmental Effects on Quantitative Biochemistry in Single Cells. Anal Chem 2023; 95:17246-17255. [PMID: 37963214 DOI: 10.1021/acs.analchem.3c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Biomacromolecules exist and function in a crowded and spatially confined intracellular milieu. Single-cell analysis has been an essential tool for deciphering the molecular mechanisms of cell biology and cellular heterogeneity. However, a sound understanding of in vivo environmental effects on single-cell quantification has not been well established. In this study, via cell mimicking with giant unilamellar vesicles and single-cell analysis by an approach called plasmonic immunosandwich assay (PISA) that we developed previously, we investigated the effects of two in vivo environmental factors, i.e., molecular crowding and spatial confinement, on quantitative biochemistry in the cytoplasm of single cells. We find that molecular crowding greatly affects the biomolecular interactions and immunorecognition-based detection while the effect of spatial confinement in cell-sized space is negligible. Without considering the effect of molecular crowding, the results by PISA were found to be apparently under-quantitated, being only 29.5-50.0% of those by the calibration curve considering the effect of molecular crowding. We further demonstrated that the use of a calibration curve established with standard solutions containing 20% (wt) polyethylene glycol 6000 can well offset the effect of intracellular crowding and thereby provide a simple but accurate calibration for the PISA measurement. Thus, this study not only sheds light on how intracellular environmental factors influence biomolecular interactions and immunorecognition-based single-cell quantification but also provides a simple but effective strategy to make the single-cell analysis more accurate.
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Affiliation(s)
- Anqi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Ge Ge
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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5
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Chen C, Song M, Li K, Yan S, Chen M, Geng J. E. coli outer membrane protein T (OmpT) nanopore for peptide sensing. Biochem Biophys Res Commun 2023; 677:132-140. [PMID: 37586211 DOI: 10.1016/j.bbrc.2023.05.125] [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: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 08/18/2023]
Abstract
Peptide detection methods with facility and high sensitivity are essential for diagnosing disease associated with peptide biomarkers. Nanopore sensing technology had emerged as a low cost, high-throughput, and scalable tool for peptide detection. The omptins family proteins which can form β-barrel pores have great potentials to be developed as nanopore biosensor. However, there are no study about the channel properties of E. coli OmpT and the development of OmpT as a nanopore biosensor. In this study, the OmpT biological nanopore channel was constructed with a conductance of 1.49 nS in 500 mM NaCl buffer and a three-step gating phenomenon under negative voltage higher than 100 mV and then was developed as a peptide biosensor which can detect peptide without the interfere of ssDNA and dNTPs. The OmpT constructed in this study has potential application in peptide detection, and also provides a new idea for the detection of peptides using the specific binding ability of protease.
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Affiliation(s)
- Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, China
| | - Mengxiao Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, 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, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China.
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6
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Punia B, Chaudhury S. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores. J Phys Chem B 2023. [PMID: 37294938 DOI: 10.1021/acs.jpcb.3c02792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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7
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Zhang X, Galenkamp NS, van der Heide NJ, Moreno J, Maglia G, Kjems J. Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor. ACS NANO 2023; 17:9167-9177. [PMID: 37127291 PMCID: PMC10184537 DOI: 10.1021/acsnano.2c12733] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Julián Moreno
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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8
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Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Lauren A Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Kelsey J Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA.
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA.
- The BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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9
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Chantipmanee N, Xu Y. Nanofluidics for chemical and biological dynamics in solution at the single molecular level. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Krishnan R S, Jana K, Shaji AH, Nair KS, Das AD, Vikraman D, Bajaj H, Kleinekathöfer U, Mahendran KR. Assembly of transmembrane pores from mirror-image peptides. Nat Commun 2022; 13:5377. [PMID: 36104348 PMCID: PMC9474448 DOI: 10.1038/s41467-022-33155-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Tailored transmembrane alpha-helical pores with desired structural and functional versatility have promising applications in nanobiotechnology. Herein, we present a transmembrane pore DpPorA, based on the natural pore PorACj, built from D-amino acid α-helical peptides. Using single-channel current recordings, we show that DpPorA peptides self-assemble into uniform cation-selective pores in lipid membranes and exhibit properties distinct from their L-amino acid counterparts. DpPorA shows resistance to protease and acts as a functional nanopore sensor to detect cyclic sugars, polypeptides, and polymers. Fluorescence imaging reveals that DpPorA forms well-defined pores in giant unilamellar vesicles facilitating the transport of hydrophilic molecules. A second D-amino acid peptide based on the polysaccharide transporter Wza forms transient pores confirming sequence specificity in stable, functional pore formation. Finally, molecular dynamics simulations reveal the specific alpha-helical packing and surface charge conformation of the D-pores consistent with experimental observations. Our findings will aid the design of sophisticated pores for single-molecule sensing related technologies. Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.
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12
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Tajparast M, Glavinovic M. Current Flow in a Cylindrical Nanopore with an Object–Implications for Virus Sensing. BIONANOSCIENCE 2022; 12:927-945. [PMID: 35607652 PMCID: PMC9117592 DOI: 10.1007/s12668-022-00990-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 11/18/2022]
Abstract
Interest is growing in nanopores as real-time, low-cost, label-free virus size sensors. To optimize their performance, we evaluate how external electric field and ion concentrations and pore wall charges influence currents and object (disk) radius-current relationship using simulations. The physics was described using the Poisson-Nernst-Planck and Navier–Stokes equations. In a charged cylindrical nanopore with a charged disk, elevated external electric field produces higher (and polarity independent) ion concentrations and greater ion current (largely migratory). Elevated external ion concentrations also lead to higher concentrations (mainly away from the pore wall), greater axial electric field especially in the disk-pore wall space, and finally larger current. At low concentrations, current is disk radius independent. The current rises as concentrations increase. Interestingly, the rise is greater for larger disks (except when the pore is blocked mechanically). Smaller cross-sectional area for current flow or volume exclusion of electrolyte by object thus cannot be universally accepted as explanations of current blockage. Ion current rises when pore wall charge density increases, but its direction is independent of charge sign. Current-disk radius relationship is also independent of pore wall charge sign. If the pore wall and disk charges have the same sign, larger current with bigger disk is due to higher counter-ion accumulation in the object-pore wall space. However, if their signs are opposite, it is largely due to elevated axial electric field in the object-pore wall space. Finally in uncharged nanopores, current diminishes when disk radius increases making them better sensors of virus size.
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13
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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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14
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Sun J, Thakur AK, Movileanu L. Current noise of a protein-selective biological nanopore. Proteomics 2022; 22:e2100077. [PMID: 34275190 PMCID: PMC8763983 DOI: 10.1002/pmic.202100077] [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: 04/25/2021] [Revised: 06/27/2021] [Accepted: 07/15/2021] [Indexed: 11/08/2022]
Abstract
1/f current noise is ubiquitous in protein pores, porins, and channels. We have previously shown that a protein-selective biological nanopore with an external protein receptor can function as a 1/f noise generator when a high-affinity protein ligand is reversibly captured by the receptor. Here, we demonstrate that the binding affinity and concentration of the ligand are key determinants for the nature of current noise. For example, 1/f was absent when a protein ligand was reversibly captured at a much lower concentration than its equilibrium dissociation constant against the receptor. Furthermore, we also analyzed the composite current noise that resulted from mixtures of low-affinity and high-affinity ligands against the same receptor. This study highlights the significance of protein recognition events in the current noise fluctuations across biological membranes.
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Affiliation(s)
- Jiaxin Sun
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Avinash Kumar Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA,The BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA,Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA,The corresponding author’s contact information: Liviu Movileanu, PhD, Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA. Phone: 315-443-8078;
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15
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Review of the use of nanodevices to detect single molecules. Anal Biochem 2022; 654:114645. [DOI: 10.1016/j.ab.2022.114645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
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16
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Mayse LA, Imran A, Larimi MG, Cosgrove MS, Wolfe AJ, Movileanu L. Disentangling the recognition complexity of a protein hub using a nanopore. Nat Commun 2022; 13:978. [PMID: 35190547 PMCID: PMC8861093 DOI: 10.1038/s41467-022-28465-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
WD40 repeat proteins are frequently involved in processing cell signaling and scaffolding large multi-subunit machineries. Despite their significance in physiological and disease-like conditions, their reversible interactions with other proteins remain modestly examined. Here, we show the development and validation of a protein nanopore for the detection and quantification of WD40 repeat protein 5 (WDR5), a chromatin-associated hub involved in epigenetic regulation of histone methylation. Our nanopore sensor is equipped with a 14-residue Win motif of mixed lineage leukemia 4 methyltransferase (MLL4Win), a WDR5 ligand. Our approach reveals a broad dynamic range of MLL4Win-WDR5 interactions and three distant subpopulations of binding events, representing three modes of protein recognition. The three binding events are confirmed as specific interactions using a weakly binding WDR5 derivative and various environmental contexts. These outcomes demonstrate the substantial sensitivity of our nanopore sensor, which can be utilized in protein analytics. Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
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17
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Liu W, Nestorovich EM. Probing Protein Nanopores with Poly(ethylene glycol)s. Proteomics 2022; 22:e2100055. [PMID: 35030301 DOI: 10.1002/pmic.202100055] [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: 07/02/2021] [Revised: 11/16/2021] [Accepted: 01/10/2022] [Indexed: 11/08/2022]
Abstract
Neutral water-soluble poly(ethylene glycol)s (PEGs) have been extensively explored in protein nanopore research for the past several decades. The principal use of PEGs is to investigate the membrane protein ion channel physical characteristics and transport properties. In addition, protein nanopores are used to study polymer-protein interactions and polymer physicochemical properties. In this review, we focus on the biophysical studies on probing protein ion channels with PEGs, specifically on nanopore sizing by PEG partitioning. We discuss the fluctuation analysis of ion channel currents in response to the PEGs moving within their confined geometries. The advantages, limitations, and recent developments of the approach are also addressed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenxing Liu
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC, 20064, USA
| | - Ekaterina M Nestorovich
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC, 20064, USA
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18
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Zhang L, Burns N, Jordan M, Jayasinghe L, Guo P. Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells. Biomater Sci 2021; 10:167-177. [PMID: 34812812 DOI: 10.1039/d1bm01264a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.
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Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Jordan
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lakmal Jayasinghe
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
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19
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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20
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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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21
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Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
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Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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22
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Al Sulaiman D, Gatehouse A, Ivanov AP, Edel JB, Ladame S. Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26673-26681. [PMID: 34085806 DOI: 10.1021/acsami.1c01145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fast sampling followed by sequence-independent sensing and length-dependent detection of short double-stranded DNA fragments, the size of those found in blood and other bodily fluids, is achieved using engineered molecular sensors, dubbed hydrogel-filled nanopores (HFNs). Fragments as short as 100 base pairs were blindly sampled and concentrated at the tip of an HFN before reversing the applied potential to detect and distinguish individual molecules based on fragment length as they translocate out of the nanopore. A remarkable 16-fold increase in the signal-to-noise ratio was observed in the eject configuration compared to the load configuration, enabling the resolution of fragments with a size difference of 50 nucleotides in length. This fast and versatile technology offers great tunability for both sampling and detection. While increasing sampling time leads to an increase in the local DNA concentration at the tip prior to detection, a linear correlation between the peak current and DNA fragment size enables good resolution of fragments up to 250 bp long.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alfie Gatehouse
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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23
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021; 7:7/17/eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.
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Affiliation(s)
| | - Joseph W F Robertson
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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24
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021; 60:14738-14749. [DOI: 10.1002/anie.202013462] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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25
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Yi‐Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
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26
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Larimi MG, Ha JH, Loh SN, Movileanu L. Insertion state of modular protein nanopores into a membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183570. [PMID: 33529578 DOI: 10.1016/j.bbamem.2021.183570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 01/04/2023]
Abstract
In the past decade, significant progress has been made in the development of new protein nanopores. Despite these advancements, there is a pressing need for the creation of nanopores equipped with relatively large functional groups for the sampling of biomolecular events on their extramembranous side. Here, we designed, produced, and analyzed protein nanopores encompassing a robust truncation of a monomeric β-barrel membrane protein. An exogenous stably folded protein was anchored within the aqueous phase via a flexible peptide tether of varying length. We have extensively examined the pore-forming properties of these modular protein nanopores using protein engineering and single-molecule electrophysiology. This study revealed distinctions in the nanopore conductance and current fluctuations that arose from tethering the exogenous protein to either the N terminus or the C terminus. Remarkably, these nanopores insert into a planar lipid membrane with one specific conductance among a set of three substate conductance values. Moreover, we demonstrate that the occurrence probabilities of these insertion substates depend on the length of the peptide tether, the orientation of the exogenous protein with respect to the nanopore opening, and the molecular mass of tethered protein. In addition, the three conductance values remain unaltered by major changes in the composition of modular nanopores. The outcomes of this work serve as a platform for further developments in areas of protein engineering of transmembrane pores and biosensor technology.
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Affiliation(s)
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA.
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27
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Sun J, Thakur AK, Movileanu L. Protein Ligand-Induced Amplification in the 1/ f Noise of a Protein-Selective Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15247-15257. [PMID: 33307706 PMCID: PMC7755739 DOI: 10.1021/acs.langmuir.0c02498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Previous studies of transmembrane protein channels have employed noise analysis to examine their statistical current fluctuations. In general, these explorations determined a substrate-induced amplification in the Gaussian white noise of these systems at a low-frequency regime. This outcome implies a lack of slowly appearing fluctuations in the number and local mobility of diffusing charges in the presence of channel substrates. Such parameters are among the key factors in generating a low-frequency 1/f noise. Here, we show that a protein-selective biological nanopore exhibits a substrate-induced amplification in the 1/f noise. The modular composition of this biological nanopore includes a hydrophilic transmembrane protein pore fused to a water-soluble binding protein on its extramembranous side. In addition, this protein nanopore shows an open substate populated by a high-frequency current noise because of the flickering of an engineered polypeptide adaptor at the tip of the pore. However, the physical association of the protein ligand with the binding domain reversibly switches the protein nanopore from a high-frequency noise substate into a quiet substate. In the absence of the protein ligand, our nanopore shows a low-frequency white noise. Remarkably, in the presence of the protein ligand, an amplified low-frequency 1/f noise was detected in a ligand concentration-dependent fashion. This finding suggests slowly occurring equilibrium fluctuations in the density and local mobility of charge carriers under these conditions. Furthermore, we report that the excess in 1/f noise is generated by reversible switches between the noisy ligand-released substate and the quiet ligand-captured substate. Finally, quantitative aspects of the low-frequency 1/f noise are in accord with theoretical predictions of the current noise analysis of protein channel-ligand interactions.
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Affiliation(s)
- Jiaxin Sun
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Avinash Kumar Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
- The corresponding author’s contact information: Liviu Movileanu, PhD, Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA. Phone: 315-443-8078; Fax: 315-443-9103;
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28
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Chau C, Radford SE, Hewitt EW, Actis P. Macromolecular Crowding Enhances the Detection of DNA and Proteins by a Solid-State Nanopore. NANO LETTERS 2020; 20:5553-5561. [PMID: 32559088 PMCID: PMC7357865 DOI: 10.1021/acs.nanolett.0c02246] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Indexed: 05/19/2023]
Abstract
Nanopore analysis of nucleic acid is now routine, but detection of proteins remains challenging. Here, we report the systematic characterization of the effect of macromolecular crowding on the detection sensitivity of a solid-state nanopore for circular and linearized DNA plasmids, globular proteins (β-galactosidase), and filamentous proteins (α-synuclein amyloid fibrils). We observe a remarkable ca. 1000-fold increase in the molecule count for the globular protein β-galactosidase and a 6-fold increase in peak amplitude for plasmid DNA under crowded conditions. We also demonstrate that macromolecular crowding facilitates the study of the topology of DNA plasmids and the characterization of amyloid fibril preparations with different length distributions. A remarkable feature of this method is its ease of use; it simply requires the addition of a macromolecular crowding agent to the electrolyte. We therefore envision that macromolecular crowding can be applied to many applications in the analysis of biomolecules by solid-state nanopores.
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Affiliation(s)
- Chalmers
C. Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric W. Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
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29
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Löwe M, Kalacheva M, Boersma AJ, Kedrov A. The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes. FEBS J 2020; 287:5039-5067. [DOI: 10.1111/febs.15429] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Maryna Löwe
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
| | | | | | - Alexej Kedrov
- Synthetic Membrane Systems Institute of Biochemistry Heinrich Heine University Düsseldorf Germany
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30
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McClintic WT, Taylor GJ, Simpson ML, Collier CP. Macromolecular Crowding Affects Voltage-Dependent Alamethicin Pore Formation in Lipid Bilayer Membranes. J Phys Chem B 2020; 124:5095-5102. [DOI: 10.1021/acs.jpcb.0c01650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William T. McClintic
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Graham J. Taylor
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Michael L. Simpson
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - C. Patrick Collier
- The Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Nanophase Material Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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31
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Zernia S, van der Heide NJ, Galenkamp NS, Gouridis G, Maglia G. Current Blockades of Proteins inside Nanopores for Real-Time Metabolome Analysis. ACS NANO 2020; 14:2296-2307. [PMID: 32003969 PMCID: PMC7045694 DOI: 10.1021/acsnano.9b09434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 05/14/2023]
Abstract
Biological nanopores are emerging as powerful and low-cost sensors for real-time analysis of biological samples. Proteins can be incorporated inside the nanopore, and ligand binding to the protein adaptor yields changes in nanopore conductance. In order to understand the origin of these conductance changes and develop sensors for detecting metabolites, we tested the signal originating from 13 different protein adaptors. We found that the quality of the protein signal depended on both the size and charge of the protein. The engineering of a dipole within the surface of the adaptor reduced the current noise by slowing the protein dynamics within the nanopore. Further, the charge of the ligand and the induced conformational changes of the adaptor defined the conductance changes upon metabolite binding, suggesting that the protein resides in an electrokinetic minimum within the nanopore, the position of which is altered by the ligand. These results represent an important step toward understanding the dynamics of the electrophoretic trapping of proteins inside nanopores and will allow developing next-generation sensors for metabolome analysis.
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Affiliation(s)
- Sarah Zernia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giorgos Gouridis
- Rega
Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Box 1037, 3000 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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32
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Yao F, Peng X, Su Z, Tian L, Guo Y, Kang XF. Crowding-Induced DNA Translocation through a Protein Nanopore. Anal Chem 2020; 92:3827-3833. [PMID: 32048508 DOI: 10.1021/acs.analchem.9b05249] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A crowded cellular environment is highly associated with many significant biological processes. However, the effect of molecular crowding on the translocation behavior of DNA through a pore has not been explored. Here, we use nanopore single-molecule analytical technique to quantify the thermodynamics and kinetics of DNA transport under heterogeneous cosolute PEGs. The results demonstrate that the frequency of the translocation event exhibits a nonmonotonic dependence on the crowding agent size, while both the event frequency and translocation time increase monotonically with increasing crowder concentration. In the presence of PEGs, the rate of DNA capture into the nanopore elevates 118.27-fold, and at the same time the translocation velocity decreases from 20 to 120 μs/base. Interestingly, the impact of PEG 4k on the DNA-nanopore interaction is the most notable, with up to ΔΔG = 16.27 kJ mol-1 change in free energy and 764.50-fold increase in the binding constant at concentration of 40% (w/v). The molecular crowding effect will has broad applications in nanopore biosensing and nanopore DNA sequencing in which the strategy to capture analyte and to control the transport is urgently required.
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Affiliation(s)
- Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao Peng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Zhuoqun Su
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
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33
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Ji Z, Jordan M, Jayasinghe L, Guo P. Insertion of channel of phi29 DNA packaging motor into polymer membrane for high-throughput sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 25:102170. [PMID: 32035271 DOI: 10.1016/j.nano.2020.102170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/25/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022]
Abstract
The connector channel of bacteriophage phi29 DNA packaging motor has been inserted into the lipid bilayer membrane and has shown potential for the sensing of DNA, RNA, chemicals, peptides, and antibodies. Properties such as high solubility and large channel size have made phi29 channel an advantageous system for those applications; however, previously studied lipid membranes have short lifetimes, and they are frangible and unstable under voltages higher than 200 mV. Thus, the application of this lipid membrane platform for clinical applications is challenging. Here we report the insertion of the connector into the stable polymer membrane in MinION flow cell that contains 2048 wells for high-throughput sensing by the liposome-polymer fusion process. The successful insertion of phi29 connector was confirmed by a unique gating phenomenon. Peptide translocation through the inserted phi29 connector was also observed, revealing the potential of applying phi29 connector for high-throughput peptide sensing.
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Affiliation(s)
- Zhouxiang Ji
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Michael Jordan
- Oxford Nanopore Technologies Limited, Oxford Science Park, UK
| | | | - Peixuan Guo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA; College of Medicine, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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Ding T, Chen AK, Lu Z. The applications of nanopores in studies of proteins. Sci Bull (Beijing) 2019; 64:1456-1467. [PMID: 36659703 DOI: 10.1016/j.scib.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023]
Abstract
Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.
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Affiliation(s)
- Taoli Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Zuhong Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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35
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Thakur AK, Movileanu L. Single-Molecule Protein Detection in a Biofluid Using a Quantitative Nanopore Sensor. ACS Sens 2019; 4:2320-2326. [PMID: 31397162 DOI: 10.1021/acssensors.9b00848] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein detection in complex biological fluids has wide-ranging significance across proteomics and molecular medicine. Existing detectors cannot readily distinguish between specific and nonspecific interactions in a heterogeneous solution. Here, we show that this daunting shortcoming can be overcome by using a protein bait-containing biological nanopore in mammalian serum. The capture and release events of a protein analyte by the tethered protein bait occur outside the nanopore and are accompanied by uniform current openings. Conversely, nonspecific pore penetrations by nontarget components of serum, which take place inside the nanopore, are featured by irregular current blockades. As a result of this unique peculiarity of the readout between specific protein captures and nonspecific pore penetration events, our selective sensor can quantitatively sample proteins at single-molecule precision in a manner distinctive from those employed by prevailing methods. Because our sensor can be integrated into nanofluidic devices and coupled with high-throughput technologies, our approach will have a transformative impact in protein identification and quantification in clinical isolates for disease prognostics and diagnostics.
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Affiliation(s)
- Avinash Kumar Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
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