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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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2
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Recent Advances in Aptamer‐Based Nanopore Sensing at Single‐Molecule Resolution. Chem Asian J 2022; 17:e202200364. [DOI: 10.1002/asia.202200364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/20/2022] [Indexed: 11/07/2022]
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3
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Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
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Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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4
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Zhu L, Zhang Z, Liu Q. Deformation-Mediated Translocation of DNA Origami Nanoplates through a Narrow Solid-State Nanopore. Anal Chem 2020; 92:13238-13245. [PMID: 32872775 DOI: 10.1021/acs.analchem.0c02396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With the development in DNA self-assembly technology, DNA origami nanostructures have been widely applied in biomedical research. Solid-state nanopores represent an emerging single-molecule sensing platform for studying nanostructures with arbitrary dimensions and physical characteristics, including DNA origami. Here, we employed relatively narrow silicon nitride nanopores to detect the deformation and translocation of DNA origami nanoplates with dimensions of approximately 60 × 54 nm. We performed translocation experiments using three nanopore diameters that are all smaller than the plat dimensions. Analysis of current blockade signals and the representative events reveals three types of translocation orientations for the nanoplates. Furthermore, by studying the electrical signal characteristics (current change and dwell time) for the different diameter pores, we obtained information about the translocation behaviors for the DNA nanoplates through different constrictions. Our investigation provides an approach to analyze the deformation and translocation of DNA origami structures.
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Affiliation(s)
- Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
| | - Zhen Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China
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5
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Liu X, Zeng Q, Liu C, Wang L. A Fourier Transform-Induced Data Process for Label-Free Selective Nanopore Analysis under Sinusoidal Voltage Excitations. Anal Chem 2020; 92:11635-11643. [PMID: 32786474 DOI: 10.1021/acs.analchem.0c01339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nanopore analysis based on a resistive-pulse technique is an attractive tool for single-molecule detection in different fields, but it suffers a great drawback in selectivity. A common solution to this challenge is to add extra sensing aptamers and labels to analytes by improving the sensitivity of their pulses for distinguishing. Compared to the labeling methods, we alternatively develop and demonstrate a novel data process for label-free nanopore analysis that enables the conversion of resistive current signals to more specific frequency domain phase angle features with the contribution from both sinusoidal voltage excitation and Fourier transform. In particular, we find that the transmural capacitance induced by nanoparticle translocations under a sinusoidal voltage plays an important role in this process, making phase angle features more pronounced. In practical applications, the method is successfully applied to directly distinguish the translocation events through a nanopipette by their unique phase angles for similarly sized SiO2, Ag, and Au nanoparticles and soft living organisms of HeLa and LoVo and even in a more complicated case of a SiO2, Ag, and Au nanoparticle mixture.
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Affiliation(s)
- Xuye Liu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Qiang Zeng
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Cheng Liu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lishi Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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6
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Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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7
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Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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8
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Kubánková M, Lin X, Albrecht T, Edel JB, Kuimova MK. Rapid Fragmentation during Seeded Lysozyme Aggregation Revealed at the Single Molecule Level. Anal Chem 2019; 91:6880-6886. [PMID: 30999745 DOI: 10.1021/acs.analchem.9b01221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation is associated with neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The poorly understood pathogenic mechanism of amyloid diseases makes early stage diagnostics or therapeutic intervention a challenge. Seeded polymerization that reduces the duration of the lag phase and accelerates fibril growth is a widespread model to study amyloid formation. Seeding effects are hypothesized to be important in the "infectivity" of amyloids and are linked to the development of systemic amyloidosis in vivo. The exact mechanism of seeding is unclear yet critical to illuminating the propagation of amyloids. Here we report on the lateral and axial fragmentation of seed fibrils in the presence of lysozyme monomers at short time scales, followed by the generation of oligomers and growth of fibrils.
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Affiliation(s)
- Markéta Kubánková
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Xiaoyan Lin
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Tim Albrecht
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K.,School of Chemistry, Edgbaston Campus , University of Birmingham , Birmingham B15 2TT , U.K
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
| | - Marina K Kuimova
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , U.K
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9
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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10
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Fraccari RL, Carminati M, Piantanida G, Leontidou T, Ferrari G, Albrecht T. High-bandwidth detection of short DNA in nanopipettes. Faraday Discuss 2018; 193:459-470. [PMID: 27711887 DOI: 10.1039/c6fd00109b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. The ease of fabrication, favourable wetting properties and low capacitance are some of the inherent advantages, for example compared to more conventional, silicon-based nanopore chips. Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. The electronics design has now been refined to include more sophisticated control features, such as integrated bias reversal and other features. Here, we exploit these capabilities and probe the translocation of short dsDNA in the 100 bp range, in different electrolytes. Single-stranded (ss) DNA of similar length are in use as capture probes, so label-free detection of their ds counterparts could therefore be of relevance in disease diagnostics.
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Affiliation(s)
- Raquel L Fraccari
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Marco Carminati
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Giacomo Piantanida
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tina Leontidou
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
| | - Giorgio Ferrari
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za, Leonardo da Vinci 32, Milano, Italy
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition, Road, London SW7 2AZ, UK.
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11
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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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12
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Verschueren DV, Yang W, Dekker C. Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes. NANOTECHNOLOGY 2018; 29:145302. [PMID: 29384130 PMCID: PMC5997186 DOI: 10.1088/1361-6528/aaabce] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report a simple and scalable technique for the fabrication of nanopore arrays on freestanding SiN and graphene membranes based on electron-beam lithography and reactive ion etching. By controlling the dose of the single-shot electron-beam exposure, circular nanopores of any size down to 16 nm in diameter can be fabricated in both materials at high accuracy and precision. We demonstrate the sensing capabilities of these nanopores by translocating dsDNA through pores fabricated using this method, and find signal-to-noise characteristics on par with transmission-electron-microscope-drilled nanopores. This versatile lithography-based approach allows for the high-throughput manufacturing of nanopores and can in principle be used on any substrate, in particular membranes made out of transferable two-dimensional materials.
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13
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Maffeo C, Aksimentiev A. Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Res 2017; 45:12125-12139. [PMID: 29059392 PMCID: PMC5716091 DOI: 10.1093/nar/gkx917] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/28/2017] [Indexed: 01/10/2023] Open
Abstract
During DNA replication, the single-stranded DNA binding protein (SSB) wraps single-stranded DNA (ssDNA) with high affinity to protect it from degradation and prevent secondary structure formation. Although SSB binds ssDNA tightly, it can be repositioned along ssDNA to follow the advancement of the replication fork. Using all-atom molecular dynamics simulations, we characterized the molecular mechanism of ssDNA association with SSB. Placed in solution, ssDNA–SSB assemblies were observed to change their structure spontaneously; such structural changes were suppressed in the crystallographic environment. Repeat simulations of the SSB–ssDNA complex under mechanical tension revealed a multitude of possible pathways for ssDNA to come off SSB punctuated by prolonged arrests at reproducible sites at the SSB surface. Ensemble simulations of spontaneous association of short ssDNA fragments with SSB detailed a three-dimensional map of local affinity to DNA; the equilibrium amount of ssDNA bound to SSB was found to depend on the electrolyte concentration but not on the presence of the acidic tips of the SSB tails. Spontaneous formation of ssDNA bulges and their diffusive motion along SSB surface was directly observed in multiple 10-µs-long simulations. Such reptation-like motion was confined by DNA binding to high-affinity spots, suggesting a two-step mechanism for SSB diffusion.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Ave, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W Clark St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Ave, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W Clark St, Urbana, IL 61801, USA.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA
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14
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Sze JYY, Ivanov AP, Cass AEG, Edel JB. Single molecule multiplexed nanopore protein screening in human serum using aptamer modified DNA carriers. Nat Commun 2017; 8:1552. [PMID: 29146902 PMCID: PMC5691071 DOI: 10.1038/s41467-017-01584-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/02/2017] [Indexed: 01/08/2023] Open
Abstract
The capability to screen a range of proteins at the single-molecule level with enhanced selectivity in biological fluids has been in part a driving force in developing future diagnostic and therapeutic strategies. The combination of nanopore sensing and nucleic acid aptamer recognition comes close to this ideal due to the ease of multiplexing, without the need for expensive labelling methods or extensive sample pre-treatment. Here, we demonstrate a fully flexible, scalable and low-cost detection platform to sense multiple protein targets simultaneously by grafting specific sequences along the backbone of a double-stranded DNA carrier. Protein bound to the aptamer produces unique ionic current signatures which facilitates accurate target recognition. This powerful approach allows us to differentiate individual protein sizes via characteristic changes in the sub-peak current. Furthermore, we show that by using DNA carriers it is possible to perform single-molecule screening in human serum at ultra-low protein concentrations. It is still a challenge for current nanopore sensing methods to differentiate multiple analytes from complex biological material. Here, the authors graft nucleic acid aptamer sequences along the backbone of a double stranded DNA carrier for the detection of multiple protein targets in human serum.
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Affiliation(s)
- Jasmine Y Y Sze
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
| | - Anthony E G Cass
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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15
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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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16
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Fraccari RL, Ciccarella P, Bahrami A, Carminati M, Ferrari G, Albrecht T. High-speed detection of DNA translocation in nanopipettes. NANOSCALE 2016; 8:7604-7611. [PMID: 26985713 DOI: 10.1039/c5nr08634e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface.
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Affiliation(s)
- Raquel L Fraccari
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, UK.
| | - Pietro Ciccarella
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za Leonardo da Vinci 32, Milano, Italy
| | - Azadeh Bahrami
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, UK.
| | - Marco Carminati
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za Leonardo da Vinci 32, Milano, Italy
| | - Giorgio Ferrari
- Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria, P.za Leonardo da Vinci 32, Milano, Italy
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, UK.
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17
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Nuttall P, Lee K, Ciccarella P, Carminati M, Ferrari G, Kim KB, Albrecht T. Single-Molecule Studies of Unlabeled Full-Length p53 Protein Binding to DNA. J Phys Chem B 2016; 120:2106-14. [DOI: 10.1021/acs.jpcb.5b11076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Philippa Nuttall
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Kidan Lee
- Department
of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Pietro Ciccarella
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Marco Carminati
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Giorgio Ferrari
- Dipartimento
di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, P.za Leonardo da Vinci 32, Milano, Italy
| | - Ki-Bum Kim
- Department
of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Tim Albrecht
- Imperial College London, Department of Chemistry, Exhibition Road, London SW7 2AZ, United Kingdom
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18
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Zahid OK, Hall AR. Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. HELIUM ION MICROSCOPY 2016. [DOI: 10.1007/978-3-319-41990-9_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Pud S, Verschueren D, Vukovic N, Plesa C, Jonsson MP, Dekker C. Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown. NANO LETTERS 2015; 15:7112-7. [PMID: 26333767 PMCID: PMC4859154 DOI: 10.1021/acs.nanolett.5b03239] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We present a novel cost-efficient method for the fabrication of high-quality self-aligned plasmonic nanopores by means of an optically controlled dielectric breakdown. Excitation of a plasmonic bowtie nanoantenna on a dielectric membrane localizes the high-voltage-driven breakdown of the membrane to the hotspot of the enhanced optical field, creating a nanopore that is automatically self-aligned to the plasmonic hotspot of the bowtie. We show that the approach provides precise control over the nanopore size and that these plasmonic nanopores can be used as single molecule DNA sensors with a performance matching that of TEM-drilled nanopores. The principle of optically controlled breakdown can also be used to fabricate nonplasmonic nanopores at a controlled position. Our novel fabrication process guarantees alignment of the nanopore with the optical hotspot of the nanoantenna, thus ensuring that pore-translocating biomolecules interact with the concentrated optical field that can be used for detection and manipulation of analytes.
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Affiliation(s)
| | | | - Nikola Vukovic
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | | | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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20
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Verschueren DV, Jonsson MP, Dekker C. Temperature dependence of DNA translocations through solid-state nanopores. NANOTECHNOLOGY 2015; 26:234004. [PMID: 25994084 PMCID: PMC4503867 DOI: 10.1088/0957-4484/26/23/234004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In order to gain a better physical understanding of DNA translocations through solid-state nanopores, we study the temperature dependence of λ-DNA translocations through 10 nm diameter silicon nitride nanopores, both experimentally and theoretically. The measured ionic conductance G, the DNA-induced ionic-conductance blockades [Formula: see text] and the event frequency Γ all increase with increasing temperature while the DNA translocation time τ decreases. G and [Formula: see text] are accurately described when bulk and surface conductances of the nanopore are considered and access resistance is incorporated appropriately. Viscous drag on the untranslocated part of the DNA coil is found to dominate the temperature dependence of the translocation times and the event rate is well described by a balance between diffusion and electrophoretic motion. The good fit between modeled and measured properties of DNA translocations through solid-state nanopores in this first comprehensive temperature study, suggest that our model captures the relevant physics of the process.
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21
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Yu JS, Lim MC, Huynh DTN, Kim HJ, Kim HM, Kim YR, Kim KB. Identifying the Location of a Single Protein along the DNA Strand Using Solid-State Nanopores. ACS NANO 2015; 9:5289-98. [PMID: 25938865 DOI: 10.1021/acsnano.5b00784] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.
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Affiliation(s)
- Jae-Seok Yu
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Min-Cheol Lim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Duyen Thi Ngoc Huynh
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Hyung-Jun Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Hyun-Mi Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Young-Rok Kim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Ki-Bum Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
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22
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Plesa C, Ruitenberg JW, Witteveen MJ, Dekker C. Detection of Individual Proteins Bound along DNA Using Solid-State Nanopores. NANO LETTERS 2015; 15:3153-8. [PMID: 25928590 DOI: 10.1021/acs.nanolett.5b00249] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA in cells is heavily covered with all types of proteins that regulate its genetic activity. Detection of DNA-bound proteins is a challenge that is well suited to solid-state nanopores as they provide a linear readout of the DNA and DNA-protein volume in the pore constriction along the entire length of a molecule. Here, we demonstrate that we can realize the detection of even individual DNA-bound proteins at the single-DNA-molecule level using solid-state nanopores. We introduce and use a new model system of anti-DNA antibodies bound to lambda phage DNA. This system provides several advantages since the antibodies bind individually, tolerate high salt concentrations, and will, because of their positive charge, not translocate through the pore unless bound to the DNA. Translocation of DNA-antibody samples reveals the presence of short 12 μs current spikes within the DNA traces, with amplitudes that are about 4.5 times larger than that of dsDNA, which are associated with individual antibodies. We conclude that transient interactions between the pore and the antibodies are the primary mechanism by which bound antibodies are observed. This work provides a proof-of-concept for how nanopores could be used for future sensing applications.
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Affiliation(s)
- Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Justus W Ruitenberg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Menno J Witteveen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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23
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Mathwig K, Albrecht T, Goluch ED, Rassaei L. Challenges of Biomolecular Detection at the Nanoscale: Nanopores and Microelectrodes. Anal Chem 2015; 87:5470-5. [DOI: 10.1021/acs.analchem.5b01167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Klaus Mathwig
- Pharmaceutical
Analysis, Groningen Research Institute of Pharmacy, University of Groningen, P.O. Box 196, 9700 AD Groningen, The Netherlands
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, Exhibition Road, South Kensington
Campus, London, SW7 2AZ, U.K
| | - Edgar D. Goluch
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 313SN, Boston, Massachusetts 02115, United States
| | - Liza Rassaei
- Department
of Chemical Engineering, Delft University of Technology, Julianalaan
136, 2628 BL Delft, The Netherlands
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24
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Marshall MM, Ruzicka J, Zahid OK, Henrich VC, Taylor EW, Hall AR. Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4582-4588. [PMID: 25839962 DOI: 10.1021/acs.langmuir.5b00457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study the binding of E. coli single-stranded binding protein (SSB) to single-stranded DNA (ssDNA) using a solid-state nanopore assay. We find that saturated nucleoprotein complexes can be distinguished easily from free SSB, ssDNA, or double-stranded DNA individually and demonstrate that the high affinity of SSB for ssDNA can be exploited to achieve high-fidelity differentiation from duplex molecules in a mixture. We then study nucleoprotein filament formation by systematically varying the amount of SSB relative to ssDNA. We observe a concomitant shift in the mean amplitude of electrical events that is consistent with weakly cooperative binding. Finally, we compare circular and linearized ssDNA saturated with SSB and use the results to infer structural details of the nucleoprotein complex.
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Affiliation(s)
- Michael M Marshall
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Jan Ruzicka
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Osama K Zahid
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Vincent C Henrich
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Ethan W Taylor
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Adam R Hall
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
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25
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Chakraborty K, Bandyopadhyay S. Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers. J Phys Chem B 2015; 119:10998-1009. [DOI: 10.1021/acs.jpcb.5b01687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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26
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Van Meervelt V, Soskine M, Maglia G. Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore. ACS NANO 2014; 8:12826-35. [PMID: 25493908 PMCID: PMC4410316 DOI: 10.1021/nn506077e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we showed that folded proteins can be internalized inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalization of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores can be used to probe conformational heterogeneity in protein:DNA interactions.
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Affiliation(s)
| | - Misha Soskine
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
| | - Giovanni Maglia
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, the Netherlands
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