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Li J, Hu R, Li X, Tong X, Yu D, Zhao Q. Tiny protein detection using pressure through solid-state nanopores. Electrophoresis 2017; 38:1130-1138. [DOI: 10.1002/elps.201600410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 12/31/2016] [Accepted: 01/01/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Ji Li
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
| | - Xiaoqing Li
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
| | - Xin Tong
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
- Collaborative Innovation Center of Quantum Matter; Beijing P. R. China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics; Peking University; Beijing P. R. China
- Collaborative Innovation Center of Quantum Matter; Beijing P. R. China
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52
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Kannam SK, Downton MT. Translational diffusion of proteins in nanochannels. J Chem Phys 2017; 146:054108. [DOI: 10.1063/1.4975161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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53
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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54
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Squires AH, Gilboa T, Torfstein C, Varongchayakul N, Meller A. Single-Molecule Characterization of DNA-Protein Interactions Using Nanopore Biosensors. Methods Enzymol 2016; 582:353-385. [PMID: 28062042 DOI: 10.1016/bs.mie.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Detection and characterization of nucleic acid-protein interactions, particularly those involving DNA and proteins such as transcription factors, enzymes, and DNA packaging proteins, remain significant barriers to our understanding of genetic regulation. Nanopores are an extremely sensitive and versatile sensing platform for label-free detection of single biomolecules. Analyte molecules are drawn to and through a nanoscale aperture by an electrophoretic force, which acts upon their native charge while in the sensing region of the pore. When the nanopore's diameter is only slightly larger than the biopolymer's cross section (typically a few nm); the latter must translocate through the pore in a linear fashion due to the constricted geometry in this region. These features allow nanopores to interrogate protein-nucleic acids in multiple sensing modes: first, by scanning and mapping the locations of binding sites along an analyte molecule, and second, by probing the strength of the bond between a protein and nucleic acid, using the native charge of the nucleic acid to apply an electrophoretic force to the complex while the protein is geometrically prevented from passing through the nanopore. In this chapter, we describe progress toward nanopore sensing of protein-nucleic acid complexes in the context of both mapping binding sites and performing force spectroscopy to determine the strength of interactions. We conclude by reviewing the strengths and challenges of the nanopore technique in the context of studying DNA-protein interactions.
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Affiliation(s)
- A H Squires
- Stanford University, Stanford, CA, United States
| | | | | | | | - A Meller
- The Technion, Haifa, Israel; Boston University, Boston, MA, United States.
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55
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Balme S, Coulon PE, Lepoitevin M, Charlot B, Yandrapalli N, Favard C, Muriaux D, Bechelany M, Janot JM. Influence of Adsorption on Proteins and Amyloid Detection by Silicon Nitride Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8916-8925. [PMID: 27506271 DOI: 10.1021/acs.langmuir.6b02048] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For the past 2 decades, emerging single-nanopore technologies have opened the route to multiple sensing applications. Besides DNA sensing, the identification of proteins and amyloids is a promising field for early diagnosis. However, the influence of the interactions between the nanopore surface and proteins should be taken into account. In this work, we have selected three proteins (avidin, lysozyme, and IgG) that exhibit different affinities with the SiNx surface, and we have also examined lysozyme amyloid. Our results show that the piranha treatment of SiNx significantly decreases protein adsorption. Moreover, we have successfully detected all proteins (pore diameter 17 nm) and shown the possibility of discriminating between denatured lysozyme and its amyloid. For all proteins, the capture rates are lower than expected, and we evidence that they are correlated with the affinity of proteins to the surface. Our result confirms that proteins interacting only with the nanopore surface wall stay long enough to be detected. For lysozyme amyloid, we show that the use of the nanopore is suitable for determining the number of monomer units even if only the proteins interacting with the nanopore are detected.
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Affiliation(s)
- Sébastien Balme
- Institut Européen des Membranes, UMR5635, Université de Montpellier CNRS ENSCM , Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pierre Eugène Coulon
- Laboratoire des Solides Irradiés, École polytechnique, Université Paris-Saclay , Route de Saclay, 91128 Palaiseau Cedex, France
| | - Mathilde Lepoitevin
- Institut Européen des Membranes, UMR5635, Université de Montpellier CNRS ENSCM , Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Benoît Charlot
- Institut d'Electronique et des Systèmes, Université de Montpellier , 34095 Montpellier Cedex 5, France
| | - Naresh Yandrapalli
- Centre d'Études d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS UMR5236 , 34293 Montpellier, France
| | - Cyril Favard
- Centre d'Études d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS UMR5236 , 34293 Montpellier, France
| | - Delphine Muriaux
- Centre d'Études d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS UMR5236 , 34293 Montpellier, France
| | - Mikhael Bechelany
- Institut Européen des Membranes, UMR5635, Université de Montpellier CNRS ENSCM , Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635, Université de Montpellier CNRS ENSCM , Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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56
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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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57
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Tan S, Gu D, Liu H, Liu Q. Detection of a single enzyme molecule based on a solid-state nanopore sensor. NANOTECHNOLOGY 2016; 27:155502. [PMID: 26937593 DOI: 10.1088/0957-4484/27/15/155502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The nanopore sensor as a high-throughput and low-cost technology can detect a single molecule in a solution. In the present study, relatively large silicon nitride (Si3N4) nanopores with diameters of ∼28 and ∼88 nm were fabricated successfully using a focused Ga ion beam. We have used solid-state nanopores with various sizes to detect the single horseradish peroxidase (HRP) molecule and for the first time analyzed single HRP molecular translocation events. In addition, a real-time monitored single enzyme molecular biochemical reaction and a translocation of the product of enzyme catalysis substrates were investigated by using a Si3N4 nanopore. Our nanopore system showed a high sensitivity in detecting single enzyme molecules and a real-time monitored single enzyme molecular biochemical reaction. This method could also be significant for studying gene expression or enzyme dynamics at the single-molecule level.
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Affiliation(s)
- ShengWei Tan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China
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58
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Beaudette P, Popp O, Dittmar G. Proteomic techniques to probe the ubiquitin landscape. Proteomics 2015; 16:273-87. [PMID: 26460060 DOI: 10.1002/pmic.201500290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/03/2015] [Accepted: 10/06/2015] [Indexed: 01/06/2023]
Abstract
Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct signals, either by adding a single ubiquitin or forming a chain of ubiquitins on the target protein. The enzymatic cascade associated with the cellular process determines the nature of the modification. Numerous efforts have been made for the identification of ubiquitin acceptor sites in the target proteins using genetic, biochemical or MS-based proteomic methods, such as affinity-based enrichment of ubiquitinated proteins, and antibody-based enrichment of modified peptides. Modern instrumentation enables quantitative MS strategies to identify and characterize hundreds of ubiquitin substrates in a single analysis making it the dominant method for ubiquitin site detection. Characterization of the interubiquitin connectivity in ubiquitin polymers has also moved into focus, with the field of targeted proteomics techniques proving invaluable for identifying and quantifying linkage types found in such polyubiquitin chains. This review seeks to provide an overview of the many MS-based proteomics techniques available for exploring this dynamic field.
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Affiliation(s)
- Patrick Beaudette
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Oliver Popp
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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59
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Squires AH, Atas E, Meller A. Genomic Pathogen Typing Using Solid-State Nanopores. PLoS One 2015; 10:e0142944. [PMID: 26562833 PMCID: PMC4643041 DOI: 10.1371/journal.pone.0142944] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based "fingerprints" of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.
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Affiliation(s)
- Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Evrim Atas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America.,Department of Biomedical Engineering, The Technion-Israel Institute of Technology, Haifa, 32000, Israel
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60
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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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61
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Niedzwiecki DJ, Lanci CJ, Shemer G, Cheng PS, Saven JG, Drndić M. Observing Changes in the Structure and Oligomerization State of a Helical Protein Dimer Using Solid-State Nanopores. ACS NANO 2015; 9:8907-8915. [PMID: 26262433 DOI: 10.1021/acsnano.5b02714] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein analysis using solid-state nanopores is challenging due to limitations in bandwidth and signal-to-noise ratio. Recent improvements of those two aspects have made feasible the study of small peptides using solid-state nanopores, which have an advantage over biological counterparts in tunability of the pore diameter. Here, we report on the detection and characterization of peptides as small as 33 amino acids. Silicon nitride nanopores with thicknesses less than 10 nm are used to provide signal-to-noise (S/N) levels up to S/N ∼ 10 at 100 kHz. We demonstrate differentiation of monomer and dimer forms of the GCN4-p1 leucine zipper, a coiled-coil structure well studied in molecular biology, and compare with the unstructured 33-residue monomer. GCN4-p1 is sequence segment associated with homodimerization of the transcription factor General Control Nonderepressible 4 (GCN4), which is involved in the control of amino acid synthesis in yeast. The differentiation between two oligomeric forms demonstrates the capabilities of improved solid-state nanopore platforms to extract structural information involving short peptide structures.
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Affiliation(s)
- David J Niedzwiecki
- Department of Physics and Astronomy, University of Pennsylvania , 209 South 33rd Street, Philadelphia, Pennsylvania 19104-6396, United States
| | - Christopher J Lanci
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Gabriel Shemer
- Department of Physics and Astronomy, University of Pennsylvania , 209 South 33rd Street, Philadelphia, Pennsylvania 19104-6396, United States
| | - Phillip S Cheng
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania , 209 South 33rd Street, Philadelphia, Pennsylvania 19104-6396, United States
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62
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Biesemans A, Soskine M, Maglia G. A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore. NANO LETTERS 2015; 15:6076-6081. [PMID: 26243210 PMCID: PMC4606981 DOI: 10.1021/acs.nanolett.5b02309] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rotaxanes, pseudorotaxanes, and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing, and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two protein stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<-50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (-100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.
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Affiliation(s)
- Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
- Corresponding author:
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63
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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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64
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Squires A, Atas E, Meller A. Nanopore sensing of individual transcription factors bound to DNA. Sci Rep 2015; 5:11643. [PMID: 26109509 PMCID: PMC4479991 DOI: 10.1038/srep11643] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/02/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.
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Affiliation(s)
- Allison Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A
| | - Evrim Atas
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A
| | - Amit Meller
- 1] Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A. [2] Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel, 32000
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