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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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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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Ghimire ML, Cox BD, Winn CA, Rockett TW, Schifano NP, Slagle HM, Gonzalez F, Bertino MF, Caputo GA, Reiner JE. Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing. ACS NANO 2022; 16:17229-17241. [PMID: 36214366 DOI: 10.1021/acsnano.2c07842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Cole A Winn
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Thomas W Rockett
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nicholas P Schifano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Hannah M Slagle
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Frank Gonzalez
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Massimo F Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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Jena H, Ahmadi Z, Kumar P, Dhawan G. Bioreducible polyethylenimine core-shell nanostructures as efficient and non-toxic gene and drug delivery vectors. Bioorg Med Chem 2022; 69:116886. [PMID: 35749840 DOI: 10.1016/j.bmc.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Low molecular weight branched polyethylenimine (LMW bPEIs 1.8 kDa) have received considerable attention for the fabrication of nucleic acid carriers due to their biocompatible and non-toxic nature. However, due to the inadequate nucleic acid complexation ability and transportation across the cell membrane, these show poor transfection efficacy, limiting their clinical applications. Therefore, to overcome these challenges, in this study, we have grafted bPEI 1.8 kDa with a disulfide bond containing hydrophobic moiety, 3-(2-pyridyldithio) propionic acid (PDPA), via amide linkages through EDC/NHS-mediated coupling to obtain N-[3-(2-pyridyldithio)] propionoyl polyethylenimine (PDPP) conjugates. The best formulation for nucleic acid transfection was evaluated after preparing a series of PDPP conjugates by varying the amount of PDPA. In an aqueous environment, these PDPP conjugates self-assembled to form spherical shaped core-shell PDPP nanostructures with size ranging from ∼188-307 nm and zeta-potential from ∼ +3 to +19 mV. The positively charged surface of the core-shell nanocomposites helps in the binding of plasmid DNA (pDNA), its transportation inside the cell, and protection against enzymes. Evaluation of PDPP/pDNA complexes on mammalian cells revealed that all these complexes showed significantly improved transfection efficacy without hampering cytocompatibility. Amongst all, the pDNA complex of PDPP-2 exhibited the best transfection efficiency (i.e. >6-fold) in comparison to pDNA complex of the native bPEI. The nanocomposites exhibited the redox responsive behavior advantageous for therapeutic delivery to the tumor cells. The core of the nanostructures facilitate the encapsulation of a hydrophobic model drug, ornidazole. In vitro drug release analysis showed a faster release rate in response to a reductant mimicking the cellular environment. Altogether, these nanostructures have great potential to co-deliver both drug and gene simultaneously in response to tumor cell reductive microenvironment in vitro and could be used as the next-generation delivery system.
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Affiliation(s)
- H Jena
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi 110019, India; CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Z Ahmadi
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - P Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
| | - G Dhawan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi 110019, India; Delhi School of Skill Enhancement & Entrepreneuship Development, Institute of Eminence, University of Delhi, Delhi-110007, India.
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5
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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Abstract
Many enzymatic activity assays are based on either (1) identifying and quantifying the enzyme with methods such as western blot or enzyme-linked substrate assay (ELISA) or (2) quantifying the enzymatic reaction by monitoring the changing levels of either product or substrate. We have generated an outer membrane protein G (OmpG)-based nanopore approach to distinguish enzyme identity as well as analyze the enzyme's catalytic activity. Here, we engineered an OmpG nanopore with a peptide cut site inserted into one of its loops to detect proteolytic behavior. In addition, we generated an OmpG nanopore with a single-stranded DNA attached to a loop for analyzing nucleolytic cleavage. This OmpG nanopore approach may be highly useful in analyzing specific enzymes in complex biological samples, or in directly determining kinetics of enzyme-substrate complex association and dissociation.
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Nanopore Enzymology to Study Protein Kinases and Their Inhibition by Small Molecules. Methods Mol Biol 2020. [PMID: 32918732 DOI: 10.1007/978-1-0716-0806-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nanopore enzymology is a powerful single-molecule technique for the label-free study of enzymes using engineered protein nanopore sensors. The technique has been applied to protein kinases, where it has enabled the full repertoire of kinase function to be observed, including: kinetics of substrate binding and dissociation, product binding and dissociation, nucleotide binding, and reversible phosphorylation. Further, minor modifications enable the screening of type I kinase inhibitors and the determination of inhibition constants in a facile and label-free manner. Here, we describe the design and production of suitably engineered protein nanopores and their use for the determination of key mechanistic parameters of kinases. We also provide procedures for the determination of inhibition constants of protein kinase inhibitors.
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Pham B, Eron SJ, Hill ME, Li X, Fahie MA, Hardy JA, Chen M. A Nanopore Approach for Analysis of Caspase-7 Activity in Cell Lysates. Biophys J 2019; 117:844-855. [PMID: 31427065 DOI: 10.1016/j.bpj.2019.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Caspases are an important protease family that coordinate inflammation and programmed cell death. Two closely related caspases, caspase-3 and caspase-7, exhibit largely overlapping substrate specificities. Assessing their proteolytic activities individually has therefore proven extremely challenging. Here, we constructed an outer membrane protein G (OmpG) nanopore with a caspase substrate sequence DEVDG grafted into one of the OmpG loops. Cleavage of the substrate sequence in the nanopore by caspase-7 generated a characteristic signal in the current recording of the OmpG nanopore that allowed the determination of the activity of caspase-7 in Escherichia coli cell lysates. Our approach may provide a framework for the activity-based profiling of proteases that share highly similar substrate specificity spectrums.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Maureen E Hill
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Xin Li
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts.
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore. Nat Commun 2018; 9:966. [PMID: 29511176 PMCID: PMC5840376 DOI: 10.1038/s41467-018-03418-2] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
There are still unmet needs in finding new technologies for biomedical diagnostic and industrial applications. A technology allowing the analysis of size and sequence of short peptide molecules of only few molecular copies is still challenging. The fast, low-cost and label-free single-molecule nanopore technology could be an alternative for addressing these critical issues. Here, we demonstrate that the wild-type aerolysin nanopore enables the size-discrimination of several short uniformly charged homopeptides, mixed in solution, with a single amino acid resolution. Our system is very sensitive, allowing detecting and characterizing a few dozens of peptide impurities in a high purity commercial peptide sample, while conventional analysis techniques fail to do so.
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11
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Wu X, Mu F, Zhao H. Synthesis and potential applications of nanoporous graphene: A review. ACTA ACUST UNITED AC 2018. [DOI: 10.11605/j.pnrs.201802003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wang S, Zhao Z, Haque F, Guo P. Engineering of protein nanopores for sequencing, chemical or protein sensing and disease diagnosis. Curr Opin Biotechnol 2017; 51:80-89. [PMID: 29232619 DOI: 10.1016/j.copbio.2017.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/17/2022]
Abstract
Biological systems contain highly-ordered structures performing diverse functions. The elegant structures of biomachines have inspired the development of nanopores as single molecule sensors. Over the years, the utility of nanopores for detecting a wide variety of analytes have rapidly emerged for sensing, sequencing and diagnostic applications. Several protein channels with diverse shapes and sizes, such as motor channels from bacteriophage Phi29, SPP1, T3, and T4, as well as α-hemolysin, MspA, aerolysin, FluA, OmpF/G, CsgG, ClyA, have been continually investigated and developed as nanopores. Herein, we focus on advances in biological nanopores for single molecule sensing and DNA sequencing from a protein engineering standpoint for changing pore sizes, altering charge distributions, enhancing sensitivity, improving stability, and imparting new detection capabilities.
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Affiliation(s)
| | - Zhengyi Zhao
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | | | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics & Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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Lepoitevin M, Ma T, Bechelany M, Janot JM, Balme S. Functionalization of single solid state nanopores to mimic biological ion channels: A review. Adv Colloid Interface Sci 2017; 250:195-213. [PMID: 28942265 DOI: 10.1016/j.cis.2017.09.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
In nature, ion channels are highly selective pores and act as gate to ensure selective ion transport, allowing ions to cross the membrane. By mimicking them, single solid state nanopore devices emerge as a new, powerful class of molecule sensors that allow for the label-free detection of biomolecules (DNA, RNA, and proteins), non-biological polymers, as well as small molecules. In this review, we exhaustively describe the fabrication and functionalization techniques to design highly robust and selective solid state nanopores. First we outline the different materials and methods to design nanopores, we explain the ionic conduction in nanopores, and finally we summarize some techniques to modify and functionalize the surface in order to obtain biomimetic nanopores, responding to different external stimuli.
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Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1180-1189. [PMID: 28341438 DOI: 10.1016/j.bbamem.2017.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/20/2017] [Accepted: 03/18/2017] [Indexed: 12/12/2022]
Abstract
β-Barrelmembrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. Computational engineering has the promise to generate βMPs with desired properties. Here we report a method for engineering novel βMPs based on the discovery of sequence motifs that predominantly interact with the cell membrane and appear in more than 75% of transmembrane strands. By replacing β1-β6 strands of the protein OmpF that lack these motifs with β1-β6 strands of OmpG enriched with these motifs and computational verification of increased stability of its transmembrane section, we engineered a novel βMP called OmpGF. OmpGF is predicted to form a monomer with a stable transmembrane region. Experimental validations showed that OmpGF could refold in vitro with a predominant β-sheet structure, as confirmed by circular dichroism. Evidence of OmpGF membrane insertion was provided by intrinsic tryptophan fluorescence spectroscopy, and its pore-forming property was determined by a dye-leakage assay. Furthermore, single-channel conductance measurements confirmed that OmpGF function as a monomer and exhibits increased conductance than OmpG and OmpF. These results demonstrated that a novel and functional βMP can be successfully engineered through strand replacement based on sequence motif analysis and stability calculation.
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Mohr N, Kappel C, Kramer S, Bros M, Grabbe S, Zentel R. Targeting cells of the immune system: mannosylated HPMA–LMA block-copolymer micelles for targeting of dendritic cells. Nanomedicine (Lond) 2016; 11:2679-2697. [DOI: 10.2217/nnm-2016-0167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background: Successful tumor immunotherapy depends on the induction of strong and sustained tumor antigen-specific immune responses by activated antigen-presenting cells (APCs) such as dendritic cells (DCs). Since nanoparticles have the potential to codeliver tumor-specific antigen and DC-stimulating adjuvant in a DC-targeting manner, we wanted to assess the suitability of mannosylated HPMA-LMA block polymers for immunotherapy. Materials & methods: Fluorescence-labeled block copolymer micelles derived from P(HPMA)-block-P(LMA) copolymers and according statistical copolymers were synthesized via RAFT polymerization, and loaded with the APC activator L18-MDP. Both types of copolymers were conjugated with D-mannose to target the mannose receptor as expressed by DCs and macrophages. The extent and specificity of micelle binding and activation of APCs was monitored using mouse spleen cells and bone marrow-derived DC (BMDC). Results: Nontargeting HPMA-LMA statistical copolymers showed strong unspecific cell binding. HPMA-LMA block copolymers bound DC only when conjugated with mannose, and in a mannose receptor-specific manner. Mannosylated HPMA-LMA block copolymers were internalized by DC. DC-targeting HPMA-LMA block copolymers mediated DC activation when loaded with L18-MDP. Conclusion: Mannosylated HPMA-LMA block copolymers are a promising candidate for the delvopment of DC-targeting nanovaccines.
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Affiliation(s)
- Nicole Mohr
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Cinja Kappel
- Department of Dermatology, University Medical Center, Johannes Gutenberg-University Mainz, Obere Zahlbacher Straße 63, 55131 Mainz, Germany
| | - Stefan Kramer
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
| | - Matthias Bros
- Department of Dermatology, University Medical Center, Johannes Gutenberg-University Mainz, Obere Zahlbacher Straße 63, 55131 Mainz, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center, Johannes Gutenberg-University Mainz, Obere Zahlbacher Straße 63, 55131 Mainz, Germany
| | - Rudolf Zentel
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55099 Mainz, Germany
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Wilson J, Sloman L, He Z, Aksimentiev A. Graphene Nanopores for Protein Sequencing. ADVANCED FUNCTIONAL MATERIALS 2016; 26:4830-4838. [PMID: 27746710 PMCID: PMC5063307 DOI: 10.1002/adfm.201601272] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups)-parts of the nuclear pore transport machinery. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide's charge density or increasing the peptide's hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids was as low as 1:8. The nanopore transport of the peptides was found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible.
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Affiliation(s)
- James Wilson
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
| | - Leila Sloman
- McGill University, 845 Rue Sherbrooke O, Montreal, QC H3A 0G4,
Canada
| | - Zhiren He
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois Urbana-Champaign,
Urbana, IL 61801, USA
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17
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Fahie MA, Yang B, Pham B, Chen M. Tuning the selectivity and sensitivity of an OmpG nanopore sensor by adjusting ligand tether length. ACS Sens 2016; 1:614-622. [PMID: 27500277 DOI: 10.1021/acssensors.6b00014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have previously shown that a biotin ligand tethered to the rim of an OmpG nanopore can be used to detect biotin-binding proteins. Here, we investigate the effect of the length of the polyethylene glycol tether on the nanopore's sensitivity and selectivity. When the tether length was increased from 2 to 45 ethylene repeats, sensitivity decreased substantially for a neutral protein streptavidin and slightly for a positively charged protein (avidin). In addition, we found that two distinct avidin binding conformations were possible when using a long tether. These conformations were sensitive to the salt concentration and applied voltage. Finally, a longer tether resulted in reduced sensitivity due to slower association for a monoclonal anti-biotin antibody. Our results highlight the importance of electrostatic, electroosmotic and electrophoretic forces on nanopore binding kinetics and sensor readout.
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Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bib Yang
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bach Pham
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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18
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19
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Fahie MA, Yang B, Mullis M, Holden MA, Chen M. Selective Detection of Protein Homologues in Serum Using an OmpG Nanopore. Anal Chem 2015; 87:11143-9. [PMID: 26451707 DOI: 10.1021/acs.analchem.5b03350] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Outer membrane protein G is a monomeric β-barrel porin that has seven flexible loops on its extracellular side. Conformational changes of these labile loops induce gating spikes in current recordings that we exploited as the prime sensing element for protein detection. The gating characteristics, open probability, frequency, and current decrease, provide rich information for analyte identification. Here, we show that two antibiotin antibodies each induced a distinct gating pattern, which allowed them to be readily detected and simultaneously discriminated by a single OmpG nanopore in the presence of fetal bovine serum. Our results demonstrate the feasibility of directly profiling proteins in real-world samples with minimal or no sample pretreatment.
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Affiliation(s)
- Monifa A Fahie
- Molecular and Cellular Biology Program and †Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Bib Yang
- Molecular and Cellular Biology Program and †Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Martin Mullis
- Molecular and Cellular Biology Program and †Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Matthew A Holden
- Molecular and Cellular Biology Program and †Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and †Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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20
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Zhou Z, Murdoch WJ, Shen Y. A linear polyethylenimine (LPEI) drug conjugate with reversible charge to overcome multidrug resistance in cancer cells. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.08.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Pederson ED, Barbalas J, Drown BS, Culbertson MJ, Keranen Burden LM, Kasianowicz JJ, Burden DL. Proximal Capture Dynamics for a Single Biological Nanopore Sensor. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Jonathan Barbalas
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Bryon S. Drown
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | | | - John J. Kasianowicz
- Semiconductor
Electronics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Daniel L. Burden
- Chemistry
Department, Wheaton College, Wheaton, Illinois 60187, United States
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22
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Fahie MA, Chen M. Electrostatic Interactions between OmpG Nanopore and Analyte Protein Surface Can Distinguish between Glycosylated Isoforms. J Phys Chem B 2015; 119:10198-206. [PMID: 26181080 DOI: 10.1021/acs.jpcb.5b06435] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The flexible loops decorating the entrance of OmpG nanopore move dynamically during ionic current recording. The gating caused by these flexible loops changes when a target protein is bound. The gating is characterized by parameters including frequency, duration, and open-pore current, and these features combine to reveal the identity of a specific analyte protein. Here, we show that OmpG nanopore equipped with a biotin ligand can distinguish glycosylated and deglycosylated isoforms of avidin by their differences in surface charge. Our studies demonstrate that the direct interaction between the nanopore and analyte surface, induced by the electrostatic attraction between the two molecules, is essential for protein isoform detection. Our technique is remarkably sensitive to the analyte surface, which may provide a useful tool for glycoprotein profiling.
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Affiliation(s)
- Monifa A Fahie
- Molecular and Cellular Biology Program and Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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23
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Pim Kinase Inhibitors Evaluated with a Single-Molecule Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Harrington L, Alexander LT, Knapp S, Bayley H. Pim Kinase Inhibitors Evaluated with a Single-Molecule Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2015; 54:8154-9. [DOI: 10.1002/anie.201503141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 11/07/2022]
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25
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Song Q, Chuan X, Chen B, He B, Zhang H, Dai W, Wang X, Zhang Q. A smart tumor targeting peptide-drug conjugate, pHLIP-SS-DOX: synthesis and cellular uptake on MCF-7 and MCF-7/Adr cells. Drug Deliv 2015; 23:1734-46. [PMID: 25853477 DOI: 10.3109/10717544.2015.1028601] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Doxorubicin (DOX) is a potent anticancer drug for the treatment of tumors, but the poor specificity and multi-drug resistance (MDR) on tumor cells have restricted its application. Here, a pH and reduction-responsive peptide-drug conjugate (PDC), pHLIP-SS-DOX, was synthesized to overcome these drawbacks. pH low insertion peptide (pHLIP) is a cell penetrating peptide (CPP) with pH-dependent transmembrane ability. And because of the unique cell membrane insertion pattern, it might reverse the MDR. The cellular uptake study showed that on both drug-sensitive MCF-7 and drug-resistant MCF-7/Adr cells, pHLIP-SS-DOX obviously facilitated the uptake of DOX at pH 6.0 and the uptake level on MCF-7/Adr cells was similar with that on MCF-7 cells, indicating that pHLIP-SS-DOX had the ability to target acidic tumor cells and reverse MDR. In vitro cytotoxicity study mediated by GSH-OEt demonstrated that the cytotoxic effect of pHLIP-SS-DOX was reduction responsive, with obvious cytotoxicity at pH 6.0; while it had poor cytotoxicity at pH 7.4, no matter with or without GSH-OEt pretreatment. This illustrated that pHLIP could deliver DOX into tumor cells with acidic microenvironment specifically and could not deliver drugs into normal cells with neutral microenvironment. In summary, pHLIP-SS-DOX is a promising strategy to target drugs to tumors and provides a possibility to overcome MDR.
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Affiliation(s)
- Qin Song
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Xingxing Chuan
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Binlong Chen
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Bing He
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Hua Zhang
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Wenbing Dai
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Xueqing Wang
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
| | - Qiang Zhang
- a State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences, Peking University , Beijing , China
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26
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Feng Y, Zhang Y, Ying C, Wang D, Du C. Nanopore-based fourth-generation DNA sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:4-16. [PMID: 25743089 PMCID: PMC4411503 DOI: 10.1016/j.gpb.2015.01.009] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 12/24/2022]
Abstract
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
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Affiliation(s)
- Yanxiao Feng
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuechuan Zhang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Cuifeng Ying
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; MOE Key Laboratory of Weak-light Nonlinear Photonics, School of Physics, Nankai University, Tianjin 300071, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Fahie M, Chisholm C, Chen M. Resolved single-molecule detection of individual species within a mixture of anti-biotin antibodies using an engineered monomeric nanopore. ACS NANO 2015; 9:1089-98. [PMID: 25575121 PMCID: PMC4958048 DOI: 10.1021/nn506606e] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Oligomeric protein nanopores with rigid structures have been engineered for the purpose of sensing a wide range of analytes including small molecules and biological species such as proteins and DNA. We chose a monomeric β-barrel porin, OmpG, as the platform from which to derive the nanopore sensor. OmpG is decorated with seven flexible loops that move dynamically to create a distinct gating pattern when ionic current passes through the pore. Biotin was chemically tethered to the most flexible one of these loops. The gating characteristic of the loop's movement in and out of the porin was substantially altered by analyte protein binding. The gating characteristics of the pore with bound targets were remarkably sensitive to molecular identity, even providing the ability to distinguish between homologues within an antibody mixture. A total of five gating parameters were analyzed for each analyte to create a unique fingerprint for each biotin-binding protein. Our exploitation of gating noise as a molecular identifier may allow more sophisticated sensor design, while OmpG's monomeric structure greatly simplifies nanopore production.
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Affiliation(s)
- Monifa Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Christina Chisholm
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Address correspondence to:
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28
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Abstract
![]()
Nanopores
are a versatile technique for the detection and characterization
of single molecules in solution. An ongoing challenge in the field
is to find methods to selectively detect specific biomolecules. In
this work we describe a new technique for sensing specific proteins
using unmodified solid-state nanopores. We engineered a double strand
of DNA by hybridizing nearly two hundred oligonucleotides to a linearized
version of the m13mp18 virus genome. This engineered double strand,
which we call a DNA carrier, allows positioning of protein binding
sites at nanometer accurate intervals along its contour via DNA conjugation
chemistry. We measure the ionic current signal of translocating DNA
carriers as a function of the number of binding sites and show detection
down to the single protein level. Furthermore, we use DNA carriers
to develop an assay for identifying a single protein species within
a protein mixture.
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Affiliation(s)
- Nicholas A W Bell
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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29
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Heller P, Mohr N, Birke A, Weber B, Reske-Kunz A, Bros M, Barz M. Directed Interactions of Block Copolypept(o)ides with Mannose-binding Receptors: PeptoMicelles Targeted to Cells of the Innate Immune System. Macromol Biosci 2015; 15:63-73. [DOI: 10.1002/mabi.201400417] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/23/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp Heller
- Institute of Organic Chemistry; Johannes Gutenberg-University; Duesbergweg 10-14 55099 Mainz Germany
| | - Nicole Mohr
- Institute of Organic Chemistry; Johannes Gutenberg-University; Duesbergweg 10-14 55099 Mainz Germany
| | - Alexander Birke
- Institute of Organic Chemistry; Johannes Gutenberg-University; Duesbergweg 10-14 55099 Mainz Germany
| | - Benjamin Weber
- Institute of Organic Chemistry; Johannes Gutenberg-University; Duesbergweg 10-14 55099 Mainz Germany
| | - Angelika Reske-Kunz
- Department of Dermatology; University Medical Center; Johannes Gutenberg-University Mainz; Obere Zahlbacher Straße 63 55131 Mainz Germany
| | - Matthias Bros
- Department of Dermatology; University Medical Center; Johannes Gutenberg-University Mainz; Obere Zahlbacher Straße 63 55131 Mainz Germany
| | - Matthias Barz
- Institute of Organic Chemistry; Johannes Gutenberg-University; Duesbergweg 10-14 55099 Mainz Germany
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30
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Liu H, Zhang W, Ma L, Fan L, Gao F, Ni J, Wang R. The improved blood–brain barrier permeability of endomorphin-1 using the cell-penetrating peptide synB3 with three different linkages. Int J Pharm 2014; 476:1-8. [DOI: 10.1016/j.ijpharm.2014.08.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/14/2014] [Accepted: 08/21/2014] [Indexed: 11/28/2022]
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31
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Han Y, Zhou S, Wang L, Guan X. Nanopore back titration analysis of dipicolinic acid. Electrophoresis 2014; 36:467-70. [PMID: 25074707 DOI: 10.1002/elps.201400255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/07/2022]
Abstract
Here, we report a novel label-free nanopore back titration method for the detection of dipicolinic acid, a marker molecule for bacterial spores. By competitive binding of the target analyte and a large ligand probe to metal ions, dipicolinic acid could be sensitively and selectively detected. This nanopore back titration approach should find useful applications in the detection of other species of medical, biological, or environmental importance if their direct detection is difficult to achieve.
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Affiliation(s)
- Yujing Han
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
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32
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Larkin J, Henley RY, Muthukumar M, Rosenstein JK, Wanunu M. High-bandwidth protein analysis using solid-state nanopores. Biophys J 2014; 106:696-704. [PMID: 24507610 DOI: 10.1016/j.bpj.2013.12.025] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 12/11/2013] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
High-bandwidth measurements of the ion current through hafnium oxide and silicon nitride nanopores allow the analysis of sub-30 kD protein molecules with unprecedented time resolution and detection efficiency. Measured capture rates suggest that at moderate transmembrane bias values, a substantial fraction of protein translocation events are detected. Our dwell-time resolution of 2.5 μs enables translocation time distributions to be fit to a first-passage time distribution derived from a 1D diffusion-drift model. The fits yield drift velocities that scale linearly with voltage, consistent with an electrophoretic process. Further, protein diffusion constants (D) are lower than the bulk diffusion constants (D0) by a factor of ~50, and are voltage-independent in the regime tested. We reason that deviations of D from D0 are a result of confinement-driven pore/protein interactions, previously observed in porous systems. A straightforward Kramers model for this inhibited diffusion points to 9- to 12-kJ/mol interactions of the proteins with the nanopore. Reduction of μ and D are found to be material-dependent. Comparison of current-blockage levels of each protein yields volumetric information for the two proteins that is in good agreement with dynamic light scattering measurements. Finally, detection of a protein-protein complex is achieved.
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Affiliation(s)
- Joseph Larkin
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Robert Y Henley
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts
| | | | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts.
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33
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Movileanu L. Watching single proteins using engineered nanopores. Protein Pept Lett 2014; 21:235-46. [PMID: 24370252 PMCID: PMC3924890 DOI: 10.2174/09298665113209990078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/03/2012] [Accepted: 11/10/2012] [Indexed: 12/22/2022]
Abstract
Recent studies in the area of single-molecule detection of proteins with nanopores show a great promise in fundamental science, bionanotechnology and proteomics. In this mini-review, I discuss a comprehensive array of examinations of protein detection and characterization using protein and solid-state nanopores. These investigations demonstrate the power of the single-molecule nanopore measurements to reveal a broad range of functional, structural, biochemical and biophysical features of proteins, such as their backbone flexibility, enzymatic activity, binding affinity as well as their concentration, size and folding state. Engineered nanopores in organic materials and in inorganic membranes coupled with surface modification and protein engineering might provide a new generation of sensing devices for molecular biomedical diagnostics.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA.
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34
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Rosen CB, Rodriguez-Larrea D, Bayley H. Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat Biotechnol 2014; 32:179-81. [PMID: 24441471 DOI: 10.1038/nbt.2799] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/12/2013] [Indexed: 01/22/2023]
Abstract
We demonstrate single-molecule, site-specific detection of protein phosphorylation with protein nanopore technology. A model protein, thioredoxin, was phosphorylated at two adjacent sites. Analysis of the ionic current amplitude and noise, as the protein unfolds and moves through an α-hemolysin pore, enables the distinction between unphosphorylated, monophosphorylated and diphosphorylated variants. Our results provide a step toward nanopore proteomics.
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Affiliation(s)
- Christian B Rosen
- 1] Department of Chemistry, University of Oxford, Oxford, UK. [2] Center for DNA Nanotechnology, Department of Chemistry and iNANO, Aarhus University, Aarhus, Denmark. [3]
| | | | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK
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35
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Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc Natl Acad Sci U S A 2013; 110:E4417-26. [PMID: 24194548 DOI: 10.1073/pnas.1312739110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In stochastic sensing, the association and dissociation of analyte molecules is observed as the modulation of an ionic current flowing through a single engineered protein pore, enabling the label-free determination of rate and equilibrium constants with respect to a specific binding site. We engineered sensors based on the staphylococcal α-hemolysin pore to allow the single-molecule detection and characterization of protein kinase-peptide interactions. We enhanced this approach by using site-specific proteolysis to generate pores bearing a single peptide sensor element attached by an N-terminal peptide bond to the trans mouth of the pore. Kinetics and affinities for the Pim protein kinases (Pim-1, Pim-2, and Pim-3) and cAMP-dependent protein kinase were measured and found to be independent of membrane potential and in good agreement with previously reported data. Kinase binding exhibited a distinct current noise behavior that forms a basis for analyte discrimination. Finally, we observed unusually high association rate constants for the interaction of Pim kinases with their consensus substrate Pimtide (~10(7) to 10(8) M(-1) · s(-1)), the result of electrostatic enhancement, and propose a cellular role for this phenomenon.
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36
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Linear-dendritic drug conjugates forming long-circulating nanorods for cancer-drug delivery. Biomaterials 2013; 34:5722-35. [DOI: 10.1016/j.biomaterials.2013.04.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/04/2013] [Indexed: 01/26/2023]
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37
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Haque F, Li J, Wu HC, Liang XJ, Guo P. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA. NANO TODAY 2013; 8:56-74. [PMID: 23504223 PMCID: PMC3596169 DOI: 10.1016/j.nantod.2012.12.008] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Beijing 100084, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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38
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Incorporation of a viral DNA-packaging motor channel in lipid bilayers for real-time, single-molecule sensing of chemicals and double-stranded DNA. Nat Protoc 2013; 8:373-92. [PMID: 23348364 DOI: 10.1038/nprot.2013.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over the past decade, nanopores have rapidly emerged as stochastic biosensors. This protocol describes the cloning, expression and purification of the channel of the bacteriophage phi29 DNA-packaging nanomotor and its subsequent incorporation into lipid membranes for single-pore sensing of double-stranded DNA (dsDNA) and chemicals. The membrane-embedded phi29 nanochannel remains functional and structurally intact under a range of conditions. When ions and macromolecules translocate through this nanochannel, reliable fingerprint changes in conductance are observed. Compared with other well-studied biological pores, the phi29 nanochannel has a larger cross-sectional area, which enables the translocation of dsDNA. Furthermore, specific amino acids can be introduced by site-directed mutagenesis within the large cavity of the channel to conjugate receptors that are able to bind specific ligands or analytes for desired applications. The lipid membrane-embedded nanochannel system has immense potential nanotechnological and biomedical applications in bioreactors, environmental sensing, drug monitoring, controlled drug delivery, early disease diagnosis and high-throughput DNA sequencing. The total time required for completing one round of this protocol is around 1 month.
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39
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Oukhaled A, Bacri L, Pastoriza-Gallego M, Betton JM, Pelta J. Sensing proteins through nanopores: fundamental to applications. ACS Chem Biol 2012; 7:1935-49. [PMID: 23145870 DOI: 10.1021/cb300449t] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteins subjected to an electric field and forced to pass through a nanopore induce blockades of ionic current that depend on the protein and nanopore characteristics and interactions between them. Recent advances in the analysis of these blockades have highlighted a variety of phenomena that can be used to study protein translocation and protein folding, to probe single-molecule catalytic reactions in order to obtain kinetic and thermodynamic information, and to detect protein-antibody complexes, proteins with DNA and RNA aptamers, and protein-pore interactions. Nanopore design is now well controlled, allowing the development of future biotechnologies and medicine applications.
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Affiliation(s)
- Abdelghani Oukhaled
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
| | - Laurent Bacri
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
| | | | - Jean-Michel Betton
- Unité de Microbiologie
Structurale, CNRS-URA 3528, Institut Pasteur, France
| | - Juan Pelta
- CNRS-UMR 8587,
LAMBE, Université de Cergy-Pontoise et Université d’Evry, France
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40
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Maier K, Martin I, Wagner E. Sequence Defined Disulfide-Linked Shuttle for Strongly Enhanced Intracellular Protein Delivery. Mol Pharm 2012; 9:3560-8. [DOI: 10.1021/mp300404d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kevin Maier
- Pharmaceutical Biotechnology, Center for System-Based Drug
Research, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Irene Martin
- Pharmaceutical Biotechnology, Center for System-Based Drug
Research, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Center for System-Based Drug
Research, and Center for Nanoscience, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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Mussi V, Fanzio P, Firpo G, Repetto L, Valbusa U. Size and functional tuning of solid state nanopores by chemical functionalization. NANOTECHNOLOGY 2012; 23:435301. [PMID: 23060606 DOI: 10.1088/0957-4484/23/43/435301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We demonstrate the possibility of using a simple functionalization procedure, based on an initial vapour-phase silanization, to control the size and functionality of solid state nanopores. The presented results show that, by varying the silanization time, it is possible to modify the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing a specific sensing selectivity. The proposed method allows us to tune the nanopore biosensor adapting it to the specific final application, and it can be efficiently applied when the pore initial diameter does not exceed a limit dimension related to the mean free path of the silane molecules at the working pressure.
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Affiliation(s)
- Valentina Mussi
- Nanomed Labs, Physics Department, University of Genova, Via Dodecaneso, 33 Genova, I-16146, Italy.
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42
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de la Escosura-Muñiz A, Merkoçi A. Nanochannels preparation and application in biosensing. ACS NANO 2012; 6:7556-83. [PMID: 22880686 DOI: 10.1021/nn301368z] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Selective transport in nanochannels (protein-based ion channels) is already used in living systems for electrical signaling in nerves and muscles, and this natural behavior is being approached for the application of biomimetic nanochannels in biosensors. On the basis of this principle, single nanochannels and nanochannel arrays seem to bring new advantages for biosensor development and applications. The purpose of this review is to provide a general comprehensive and critical overview on the latest trends in the development of nanochannel-based biosensing systems. A detailed description and discussion of representative and recent works covering the main nanochannel fabrication techniques, nanoporous material characterizations, and especially their application in both electrochemical and optical sensing systems is given. The state-of-the-art of the developed technology may open the way to new advances in the integration of nanochannels with (bio)molecules and synthetic receptors for the development of novel biodetection systems that can be extended to many other applications with interest for clinical analysis, safety, and security as well as environmental and other industrial studies and applications.
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Affiliation(s)
- Alfredo de la Escosura-Muñiz
- Nanobioelectronics & Biosensors Group, CIN2, ICN-CSIC, Catalan Institute of Nanotechnology, Campus UAB, Bellaterra, Barcelona, Spain
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43
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Soskine M, Biesemans A, Moeyaert B, Cheley S, Bayley H, Maglia G. An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. NANO LETTERS 2012; 12:4895-900. [PMID: 22849517 PMCID: PMC3440510 DOI: 10.1021/nl3024438] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopores have been used in label-free single-molecule studies, including investigations of chemical reactions, nucleic acid analysis, and applications in sensing. Biological nanopores generally perform better than artificial nanopores as sensors, but they have disadvantages including a fixed diameter. Here we introduce a biological nanopore ClyA that is wide enough to sample and distinguish large analyte proteins, which enter the pore lumen. Remarkably, human and bovine thrombins, despite 86% sequence identity, elicit characteristic ionic current blockades, which at -50 mV differ in their main current levels by 26 ± 1 pA. The use of DNA aptamers or hirudin as ligands further distinguished the protein analytes. Finally, we constructed ClyA nanopores decorated with covalently attached aptamers. These nanopores selectively captured and internalized cognate protein analytes but excluded noncognate analytes, in a process that resembles transport by nuclear pores.
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Affiliation(s)
- Misha Soskine
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | | | - Stephen Cheley
- Department of Pharmacology, University of Alberta, Edmonton, T6G 2E1, AB Canada
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
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Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J Am Chem Soc 2012; 134:2781-7. [PMID: 22229655 PMCID: PMC3278221 DOI: 10.1021/ja2105653] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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Protein nanopores have been used as stochastic sensors
for the
detection of analytes that range from small molecules to proteins.
In this approach, individual analyte molecules modulate the ionic
current flowing through a single nanopore. Here, a new type of stochastic
sensor based on an αHL pore modified with an aptamer is described.
The aptamer is bound to the pore by hybridization to an oligonucleotide
that is attached covalently through a disulfide bond to a single cysteine
residue near a mouth of the pore. We show that the binding of thrombin
to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex,
alters the ionic current through the pore. The approach allows the
quantification of nanomolar concentrations of thrombin, and provides
association and dissociation rate constants and equilibrium dissociation
constants for thrombin·aptamer interactions. Aptamer-based nanopores
have the potential to be integrated into arrays for the parallel detection
of multiple analytes.
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Affiliation(s)
- Dvir Rotem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
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Winters-Hilt S, Horton-Chao E, Morales E. The NTD Nanoscope: potential applications and implementations. BMC Bioinformatics 2011; 12 Suppl 10:S21. [PMID: 22166072 PMCID: PMC3236844 DOI: 10.1186/1471-2105-12-s10-s21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers. RESULTS The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned. CONCLUSIONS SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.
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Affiliation(s)
- Stephen Winters-Hilt
- Dept of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.
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Hattori Y, Nagaoka Y, Kubo M, Yamasaku H, Ishii Y, Okita H, Nakano H, Uesato S, Maitani Y. Antitumor Effect of Liposomal Histone Deacetylase Inhibitor-Lipid Conjugates in Vitro. Chem Pharm Bull (Tokyo) 2011; 59:1386-92. [DOI: 10.1248/cpb.59.1386] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Yasuo Nagaoka
- Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Manami Kubo
- Institute of Medicinal Chemistry, Hoshi University
| | | | - Yuta Ishii
- Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Hiroko Okita
- Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Hiroki Nakano
- Faculty of Chemistry, Materials and Bioengineering, Kansai University
| | - Shinichi Uesato
- Faculty of Chemistry, Materials and Bioengineering, Kansai University
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Mussi V, Fanzio P, Repetto L, Firpo G, Scaruffi P, Stigliani S, Menotta M, Magnani M, Tonini GP, Valbusa U. Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454104. [PMID: 21339592 DOI: 10.1088/0953-8984/22/45/454104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present data concerning the electrical properties of a class of biosensor devices based on bio-functionalized solid state nanopores able to detect different kinds of interactions between probe molecules, chemically attached to the pore surface, and target molecules present in solution and electrophoretically drawn through the nanometric channel. The great potentiality of this approach resides in the fact that the functionalization of a quite large pore (up to 50-60 nm) allows a sufficient diameter reduction for the attainment of a single molecule sensing dimension and selective activation, without the need for further material deposition, such as metal or oxides, or localized surface modification. The results indicate that it will be possible, in the near future, to conceive and design devices for parallel analysis of biological samples made of arrays of nanopores differently functionalized, fabricated by standard lithographic techniques, with important applications in the field of molecular diagnosis.
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Affiliation(s)
- V Mussi
- Nanomed Labs, Physics Department, University of Genova, and Nanobiotechnologies, National Institute of Cancer Research (IST), Largo R Benzi, 10 Genova, 16132, Italy.
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Wang HY, Ying YL, Li Y, Long YT. Peering into Biological Nanopore: A Practical Technology to Single-Molecule Analysis. Chem Asian J 2010; 5:1952-61. [DOI: 10.1002/asia.201000279] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Affiliation(s)
- Long Ma
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, UK
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50
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Caruana DJ, Howorka S. Biosensors and biofuel cells with engineered proteins. MOLECULAR BIOSYSTEMS 2010; 6:1548-56. [DOI: 10.1039/c004951d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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