1
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Ji CM, Feng XY, Huang YW, Chen RA. The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research. Viruses 2024; 16:798. [PMID: 38793679 PMCID: PMC11125791 DOI: 10.3390/v16050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.
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Affiliation(s)
- Chun-Miao Ji
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Xiao-Yin Feng
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Yao-Wei Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
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2
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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3
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Kadam P, Khisti M, Ravishankar V, Barvkar V, Dhotre D, Sharma A, Shouche Y, Zinjarde S. Recent advances in production and applications of ectoine, a compatible solute of industrial relevance. BIORESOURCE TECHNOLOGY 2024; 393:130016. [PMID: 37979886 DOI: 10.1016/j.biortech.2023.130016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Extremophilic bacteria growing in saline ecosystems are potential producers of biotechnologically important products including compatible solutes. Ectoine/hydroxyectoine are two such solutes that protect cells and associated macromolecules from osmotic, heat, cold and UV stress without interfering with cellular functions. Since ectoine is a high value product, overviewing strategies for improving yields become relevant. Screening of natural isolates, use of inexpensive substrates and response surface methodology approaches have been used to improve bioprocess parameters. In addition, genome mining exercises can aid in identifying hitherto unreported microorganisms with a potential to produce ectoine that can be exploited in the future. Application wise, ectoine has various biotechnological (protein protectant, membrane modulator, DNA protectant, cryoprotective agent, wastewater treatment) and biomedical (dermatoprotectant and in overcoming respiratory and hypersensitivity diseases) uses. The review summarizes current updates on the potential of microorganisms in the production of this industrially relevant metabolite and its varied applications.
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Affiliation(s)
- Pratik Kadam
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Mitesh Khisti
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Varun Ravishankar
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India
| | - Vitthal Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune,411007, India
| | - Dhiraj Dhotre
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India
| | - Avinash Sharma
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India; School of Agriculture, Graphic Era Hill University, Dehradun, India
| | - Yogesh Shouche
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune,411007, India; SKAN Research Center, Bengaluru, India
| | - Smita Zinjarde
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune,411007, India.
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4
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Zhang Y, Yi Y, Li Z, Zhou K, Liu L, Wu HC. Peptide sequencing based on host-guest interaction-assisted nanopore sensing. Nat Methods 2024; 21:102-109. [PMID: 37957431 DOI: 10.1038/s41592-023-02095-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Direct protein sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose an alternative method for peptide sequencing based on enzymatic cleavage and host-guest interaction-assisted nanopore sensing. We serendipitously discovered that the identity of any proteinogenic amino acid in a particular position of a phenylalanine-containing peptide could be determined via current blockage during translocation of the peptide through α-hemolysin nanopores in the presence of cucurbit[7]uril. Building upon this, we further present a proof-of-concept demonstration of peptide sequencing by sequentially cleaving off amino acids from C terminus of a peptide with carboxypeptidases, and then determining their identities and sequence with a peptide probe in nanopore. With future optimization, our results point to a different way of nanopore-based protein sequencing.
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Affiliation(s)
- Yun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yakun Yi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Seth S, Bhattacharya A. DNA Barcodes Using a Dual Nanopore Device. Methods Mol Biol 2024; 2744:197-211. [PMID: 38683320 DOI: 10.1007/978-1-0716-3581-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.
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6
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van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C. Genomics in the long-read sequencing era. Trends Genet 2023; 39:649-671. [PMID: 37230864 DOI: 10.1016/j.tig.2023.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
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Affiliation(s)
- Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kévin Gorrichon
- National Center of Human Genomics Research (CNRGH), 91000 Évry-Courcouronnes, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rania Ouazahrou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Céline Hernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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7
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Schuhmacher M, Hoogendoorn S. Out With a Bang: Celebrating Global Chemical Biology. ACS Chem Biol 2023; 18:218-222. [PMID: 36648442 DOI: 10.1021/acschembio.2c00905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
On November 8-10, 2022, 163 participants from all over the world gathered at the Campus Biotech in Geneva, Switzerland to share in the latest research in chemical biology. The fourth international symposium of the Swiss National Centres of Competence in Research (NCCR) Chemical Biology coincided with the end of this successful research consortium, and as such this event marked a celebration of the past 12 years of chemical biology research in Switzerland. The inspiring talks delivered by the 15 well-known scientists, balanced in gender, expertise, and geographic location, as well as the numerous poster presentations by junior scientists showcased the breadth of global chemical biology and the bright future ahead.
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Affiliation(s)
- Milena Schuhmacher
- Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sascha Hoogendoorn
- Department of Organic Chemistry, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland
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8
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. MICROMACHINES 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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9
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Hu WH, Zhou K, Liu L, Wu HC. Construction of a pH-Mediated Single-Molecule Switch with a Nanopore-DNA Complex. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201650. [PMID: 35723176 DOI: 10.1002/smll.202201650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Indexed: 06/15/2023]
Abstract
A molecular switch is one of the simplest examples of artificial molecular machines. Even so, the development of molecular switches is still at its very early stage. Currently, building single-molecule switches mostly rely on the molecular junction technique, but many of their performance characteristics are device-dependent. Here, a pH-mediated single-molecule switch based on the combination of an α-hemolysin (αHL) nanopore and a hexacyclen-modified DNA strand is developed. The single-stranded DNA is suspended inside an αHL through biotin-streptavidin linkage and the hexacyclen-modified nucleobase interacts with amino acid residues at positions 111, 113, and 147 to cause current oscillations. Distinct current transitions are observed when pH is tuned back and forth in the range of 3.0-7.4, with a typical "up" level when pH > 6.5 and a "down" level when pH < 4.5. This nanopore-DNA complex possesses membrane-bound advantages and may find applications in single-cell studies where pH could be readily tuned to control ON-OFF functions.
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Affiliation(s)
- Wei-Hu Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Seth S, Bhattacharya A. How capture affects polymer translocation in a solitary nanopore. J Chem Phys 2022; 156:244902. [DOI: 10.1063/5.0094221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in the presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way toward the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture, while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidence of the interpretation of the experimentally observed folds [M. Gershow and J. A. Golovchenko, Nat. Nanotechnol. 2, 775 (2007) and Mihovilovic et al., Phys. Rev. Lett. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding—that a charged tag attached at the 5′ end of the DNA enhances both the multi-scan rate and the uni-directional translocation (5′ → 3′) probability that would benefit the genomic barcoding and sequencing experiments.
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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11
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Xu C, Lei C, Hosseinpour S, Ivanovski S, Walsh LJ, Khademhosseini A. Nanotechnology for the management of COVID-19 during the pandemic and in the post-pandemic era. Natl Sci Rev 2022; 9:nwac124. [PMID: 36196115 PMCID: PMC9522393 DOI: 10.1093/nsr/nwac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/12/2022] Open
Abstract
Following the global COVID-19 pandemic, nanotechnology has been at the forefront of research efforts and enables the fast development of diagnostic tools, vaccines and antiviral treatment for this novel virus (SARS-CoV-2). In this review, we first summarize nanotechnology with regard to the detection of SARS-CoV-2, including nanoparticle-based techniques such as rapid antigen testing, and nanopore-based sequencing and sensing techniques. Then we investigate nanotechnology as it applies to the development of COVID-19 vaccines and anti-SARS-CoV-2 nanomaterials. We also highlight nanotechnology for the post-pandemic era, by providing tools for the battle with SARS-CoV-2 variants and for enhancing the global distribution of vaccines. Nanotechnology not only contributes to the management of the ongoing COVID-19 pandemic but also provides platforms for the prevention, rapid diagnosis, vaccines and antiviral drugs of possible future virus outbreaks.
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Affiliation(s)
- Chun Xu
- School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
- Centre for Orofacial Regeneration, Reconstruction and Rehabilitation (COR3), School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
| | - Chang Lei
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , St Lucia, QLD 4072 , Australia
| | - Sepanta Hosseinpour
- School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
- Centre for Orofacial Regeneration, Reconstruction and Rehabilitation (COR3), School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
| | - Saso Ivanovski
- School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
- Centre for Orofacial Regeneration, Reconstruction and Rehabilitation (COR3), School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
| | - Laurence J Walsh
- School of Dentistry, The University of Queensland , Brisbane , Queensland 4006 , Australia
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation , Los Angeles , CA 90064 , USA
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12
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Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
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Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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13
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Qing Y, Bayley H. Enzymeless DNA Base Identification by Chemical Stepping in a Nanopore. J Am Chem Soc 2021; 143:18181-18187. [PMID: 34669377 DOI: 10.1021/jacs.1c07497] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stepwise movement of a single biopolymer strand through a nanoscopic detector for the sequential identification of its building blocks offers a universal means for single-molecule sequencing. This principle has been implemented in portable sequencers that use enzymes to move DNA or RNA through hundreds of individual nanopore detectors positioned in an array. Nevertheless, its application to the sequencing of other biopolymers, including polypeptides and polysaccharides, has not progressed because suitable enzymes are lacking. Recently, we devised a purely chemical means to move molecules processively in steps comparable to the repeat distances in biopolymers. Here, with this chemical approach, we demonstrate sequential nucleobase identification during DNA translocation through a nanopore. Further, the relative location of a guanine modification with a chemotherapeutic platinum derivative is pinpointed with single-base resolution. After further development, chemical translocation might replace stepping by enzymes for highly parallel single-molecule biopolymer sequencing.
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Affiliation(s)
- Yujia Qing
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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14
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 512] [Impact Index Per Article: 170.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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15
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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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Yadav P, Cao Z, Barati Farimani A. DNA Detection with Single-Layer Ti 3C 2 MXene Nanopore. ACS NANO 2021; 15:4861-4869. [PMID: 33660990 DOI: 10.1021/acsnano.0c09595] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanopore based sequencing is an exciting alternative to the conventional sequencing methods as it allows for high-throughput sequencing with lower reagent costs and time requirements. Biological nanopores, such as α-hemolysin, are subject to breakdown under thermal, electrical, and mechanical stress after being used millions of times. On the contrary, two-dimensional (2D) nanomaterials have been explored as a solid-state platform for the sequencing of DNA. Their subnanometer thickness and outstanding mechanical properties have made possible the high-resolution and high-signal-to-noise ratio detection of DNA, but such a performance is dependent on the type of nanomaterial selected. Solid-state nanopores of graphene, Si3N4, and MoS2 have been studied as potential candidates for DNA detection. However, it is important to understand the sensitivity and characterization of these solid-state materials for nanopore based detection. Recent developments in the synthesis of MXene have inspired our interest in its application as a nanopore based DNA detection membrane. Here, we simulate the metal carbide, MXene (Ti3C2), with single stranded DNA to understand its interactions and the efficiency of MXene as a putative material for the development of a nanopore based detection platform. Using molecular dynamics (MD) simulations, we present evidence that a MXene based nanopore is able to detect the different types of DNA bases. We have successfully identified features to differentiate the translocation of different types of DNA bases across the nanopore.
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Rattu P, Belzunces B, Haynes T, Skylaris CK, Khalid S. Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions. NANOSCALE 2021; 13:1673-1679. [PMID: 33434242 DOI: 10.1039/d0nr04890a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored. Our results show that aromatic residues slow down DNA translocation, and in the case of short DNA strands, they cause deviations from a linear DNA conformation. When DNA is under tension, translocation is once again slower when aromatic residues are present in the constriction. However, the lack of flexibility in the DNA backbone provides a narrower window of opportunity for the DNA bases to be retained inside the pore via interaction with the aromatic residues, compared to more flexible strands. Consequently, there is more variability in translocation rates for strands under tension. DNA entry into the pores is correlated to pore width, but no such correlation between width and translocation rate is observed.
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Affiliation(s)
- Punam Rattu
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK.
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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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Anreiter I, Mir Q, Simpson JT, Janga SC, Soller M. New Twists in Detecting mRNA Modification Dynamics. Trends Biotechnol 2021; 39:72-89. [PMID: 32620324 PMCID: PMC7326690 DOI: 10.1016/j.tibtech.2020.06.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022]
Abstract
Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.
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Affiliation(s)
- Ina Anreiter
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Topological analysis of single-stranded DNA with an alpha-hederin nanopore. Biosens Bioelectron 2020; 171:112711. [PMID: 33059170 DOI: 10.1016/j.bios.2020.112711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 11/23/2022]
Abstract
Nanopores have been emerged as a powerful tool for analyzing the structural information and interactional properties of a range of biomolecules. The spatial resolution of nanopore is determined by the diameter and effective thickness of its constriction region, but the presence of vestibule or stem structure in protein-based nanopore could negatively affect the sensitivity of the nanopore when applied for genome sequencing and topological analysis of DNA. Recently, alpha-hederin (Ah) has been reported to form a sub-nanometer scale pore structure in lipid membrane. With the simple structure and extremely small effective thickness, the Ah nanopore was shown to discriminate four different types of nucleotides. However, identification of a certain nucleotide in a strand of DNA, which is essential for genome sequencing, remains challenging. Here, we investigated the resolving capability of Ah nanopore to discriminate few nucleotides in a strand of single-stranded DNA, and the factors determining the sensitivity of Ah nanopore. The Ah nanopore was shown to be able to identify as few as three adenosine nucleotides in a strand of poly cytidine, in which the dwell time of the additional current blockade that represents the adenosine residue was in good agreement with their physical length. We also found that the lateral tension and chain pressure generated around the nanopore were influenced by pore's diameter and played as a dependent variables to determine the geometry of nanopore's constriction as well as the spatial resolution of the Ah nanopore.
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Zhou W, Qiu H, Guo Y, Guo W. Molecular Insights into Distinct Detection Properties of α-Hemolysin, MspA, CsgG, and Aerolysin Nanopore Sensors. J Phys Chem B 2020; 124:1611-1618. [PMID: 32027510 DOI: 10.1021/acs.jpcb.9b10702] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein nanopores have been widely used as single-molecule sensors for the detection and characterization of biological polymers such as DNA, RNA, and polypeptides. A variety of protein nanopores with various geometries have been exploited for this purpose, which usually exhibit distinct sensing capabilities, but the underlying molecular mechanism remains elusive. Here, we systematically characterize the molecular transport properties of four widely studied protein nanopores, α-hemolysin, MspA, CsgG, and aerolysin, by extensive molecular dynamics simulations. It is found that a sudden drop in electrostatic potentials occurs at the sole constriction in MspA and CsgG nanopores in contrast to the gradual potential change inside α-hemolysin and aerolysin pores, indicating the crucial role of pore geometry in ionic and molecular transport. We further demonstrate that these protein nanopores exhibit open-pore currents and ssDNA-induced current blockades both in the order MspA > α-hemolysin > CsgG > aerolysin, but an equivalent blockade percentage around 80%. In addition, the substitution of key amino acids at the pore constriction, especially by charged ones, provides an efficient way to modulate the pore electrostatic potential and ionic current. This work sheds new light on the search for high-performance nanopores, engineering of protein nanopores, and design of bioinspired solid-state nanopores.
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Affiliation(s)
- Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yufeng Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore. Nat Commun 2019; 10:5668. [PMID: 31827098 PMCID: PMC6906327 DOI: 10.1038/s41467-019-13677-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
Biological nanopores are capable of resolving small analytes down to a monoatomic ion. In this research, tetrachloroaurate(III), a polyatomic ion, is discovered to bind to the methionine residue (M113) of a wild-type α-hemolysin by reversible Au(III)-thioether coordination. However, the cylindrical pore geometry of α-hemolysin generates shallow ionic binding events (~5–6 pA) and may have introduced other undesired interactions. Inspired by nanopore sequencing, a Mycobacterium smegmatis porin A (MspA) nanopore, which possesses a conical pore geometry, is mutated to bind tetrachloroaurate(III). Subsequently, further amplified blockage events (up to ~55 pA) are observed, which report the largest single ion binding event from a nanopore measurement. By taking the embedded Au(III) as an atomic bridge, the MspA nanopore is enabled to discriminate between different biothiols from single molecule readouts. These phenomena suggest that MspA is advantageous for single molecule chemistry investigations and has applications as a hybrid biological nanopore with atomic adaptors. Engineered biological nanopores enable observation of single molecule chemistry events; however a cylindrical pore geometry can have undesired effects. The authors report a conical biological pore which was embedded with tetrachloroaurate(III) to allow for discrimination between different biothiols.
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Reeve MA, Bachmann D. MALDI-TOF MS protein fingerprinting of mixed samples. Biol Methods Protoc 2019; 4:bpz013. [PMID: 32395630 PMCID: PMC7200911 DOI: 10.1093/biomethods/bpz013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Abstract
Analytical techniques currently available for the characterization of mixtures of microorganisms are generally based on next-generation sequencing. Motivated to develop practical and less-expensive methods for characterizing such mixtures, we propose, as an alternative or complement, the use of matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS), which is capable of high-resolution discrimination between species and even between biotypes within species. Potential approaches employing this technique for such characterization are discussed along with impediments to their successful employment. As a consequence, our rationale has been to capitalize on the powerful algorithms currently available for spectral comparison. Following this rationale, the first priority is to ensure the generation of MALDI-TOF MS spectra from mixtures of microorganisms that contain manageable peak complexities and that can be handled by the existing spectral comparison algorithms, preferably with the option to archive and re-run sample preparations and to pipette replicates of these onto MALDI-TOF MS sample plates. The second priority is to ensure that database entry is comparably facile to sample preparation so that large databases of known microorganism mixture MALDI-TOF MS spectra could be readily prepared for comparison with the spectra of unknown mixtures. In this article, we address the above priorities and generate illustrative MALDI-TOF MS spectra to demonstrate the utility of this approach. In addition, we investigate methods aimed at chemically modulating the peak complexity of the obtained MALDI-TOF MS spectra.
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Affiliation(s)
- Michael A Reeve
- Department of Bioscience, CABI Bioscience, Bakeham Lane, Egham, Surrey TW20 9TY, UK
| | - Denise Bachmann
- Department of Bioscience, CABI Bioscience, Bakeham Lane, Egham, Surrey TW20 9TY, UK
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MALDI-TOF MS-Based Analysis of Seed Proteins from Catalogue Varieties of Solanum lycopersicum/Lycopersicon esculentum. HORTICULTURAE 2019. [DOI: 10.3390/horticulturae5030048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Matrix-assisted laser-desorption and ionization time-of-flight mass spectroscopy (MALDI-TOF MS) is a flexible technique for the analysis of protein-containing biological samples. Simple and inexpensive methods have previously been developed for MALDI-TOF MS sample preparation that are able to discriminate between Impatiens species that are closely related and also between regional biotypes of the invasive weed Impatiens glandulifera (Himalayan balsam) with leaf material and also seed material. The current article investigates whether MALDI-TOF MS, through acid-soluble protein ‘fingerprinting’, can be used to analyze plant seeds that result from intensive commercial plant-breeding activity. As an initial proof-of-concept study, tomato seeds from eleven seed-catalogue varieties (F1 Pink Baby Plum, F1 Fantasio, F1 Lizzano, F1 Sungold, F1 Tumbler, Faworyt, Golden Sunrise, Hundreds and Thousands, Indigo Rose, Moneymaker, and Red Alert), listed as Solanum lycopersicum or under the synonym Lycopersicon esculentum were analyzed using MALDI-TOF MS. Whilst peak-rich and highly-reproducible spectra were obtained, with very high Bruker comparison scores and low MALDI-TOF MS variance, sample-preparation variance, and seed-to-seed variance, the spectral differences between varieties were only slightly greater than the above combined variances, indicating very close similarity between all eleven varieties studied. These results are discussed in comparison with those previously observed with the naturally-evolving invasive species I. glandulifera.
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Haugland MM, Borsley S, Cairns-Gibson DF, Elmi A, Cockroft SL. Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms. ACS NANO 2019; 13:4101-4110. [PMID: 30864781 DOI: 10.1021/acsnano.8b08691] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.
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Affiliation(s)
- Marius M Haugland
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Stefan Borsley
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Dominic F Cairns-Gibson
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Alex Elmi
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | - Scott L Cockroft
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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Reeve MA, Pollard KM. Discrimination between regional biotypes of Impatiens glandulifera using a simple MALDI-TOF MS-based method for use with seeds. PLANT METHODS 2019; 15:25. [PMID: 30911324 PMCID: PMC6416845 DOI: 10.1186/s13007-019-0412-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND We have recently developed a simple, rapid, and relatively-cheap method for matrix-assisted laser-desorption and ionisation time-of-flight mass spectroscopy (MALDI-TOF MS) sample preparation that is applicable to plant material (in addition to microbial and insect material), and have used this to discriminate between closely-related Impatiens species and between regional biotypes of the invasive weed Impatiens glandulifera (commonly known as Himalayan balsam) using leaf samples. In the current paper, we have developed a complementary MALDI-TOF MS-based method for use with seeds. We have employed a combination of principal-component analysis and blind-tested comparison between reference-sample MALDI-TOF MS spectra and test-sample spectra to discriminate, on the basis of the acid-soluble seed-protein spectra generated by our method, between four regional biotypes of I. glandulifera from within the UK that differ in their susceptibility to the biological control agent Himalayan balsam rust (Puccinia komarovii var. glanduliferae). RESULTS Peak-rich and highly-reproducible spectra were obtained and, in blind testing with test seeds collected in 2017 against reference seeds collected in 2017, we observed 100% identification accuracy in 12 blind tests. In blind testing with test seeds collected in 2016 against reference seeds collected in 2017, we observed 92% identification accuracy in 12 blind tests. CONCLUSIONS MALDI-TOF MS analysis of seed material is able to discriminate between regional biotypes of I. glandulifera. MALDI-TOF MS therefore has the potential to improve the efficiency and efficacy of weed biological control using co-evolved natural enemies of invasive non-native plant species, through the matching of biological control agents with susceptible regional biotypes.
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Sahu S, Zwolak M. Colloquium: Ionic phenomena in nanoscale pores through 2D materials. REVIEWS OF MODERN PHYSICS 2019; 91:10.1103/RevModPhys.91.021004. [PMID: 31579274 PMCID: PMC6774369 DOI: 10.1103/revmodphys.91.021004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS2), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and constrictions within these materials is a distinct realm of competing many-particle interactions (e.g., solvation/dehydration, electrostatic blockade, hydrogen bond dynamics) and confinement. This opens up alternative routes to creating biomimetic pores and may even give analogues of quantum phenomena, such as quantized conductance, in the classical domain. These prospects make membranes of 2D materials - i.e., 2D membranes - fascinating. We will discuss the physics and applications of ionic transport through nanopores in 2D membranes.
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Affiliation(s)
- Subin Sahu
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, USA
| | - Michael Zwolak
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The Third Revolution in Sequencing Technology. Trends Genet 2018; 34:666-681. [PMID: 29941292 DOI: 10.1016/j.tig.2018.05.008] [Citation(s) in RCA: 573] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022]
Abstract
Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.
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Affiliation(s)
- Erwin L van Dijk
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Université Paris-Sud, Université Paris-Saclay, 9198 Gif sur Yvette Cedex, France.
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Université Paris-Sud, Université Paris-Saclay, 9198 Gif sur Yvette Cedex, France
| | - Delphine Naquin
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Université Paris-Sud, Université Paris-Saclay, 9198 Gif sur Yvette Cedex, France
| | - Claude Thermes
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Université Paris-Sud, Université Paris-Saclay, 9198 Gif sur Yvette Cedex, France
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Jou I, Muthukumar M. Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA. Biophys J 2017; 113:1664-1672. [PMID: 29045861 DOI: 10.1016/j.bpj.2017.08.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/11/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022] Open
Abstract
We have investigated the dynamics of single-stranded DNA as it translocates through charge-mutated protein nanopores. Translocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over translocation speed remains one of the main challenges. Taking advantage of the interactions between negatively charged DNA and positively charged amino acid residues, the translocation speed of DNA can be manipulated by deliberate charge decorations inside the nanopore. We employed coarse-grained Langevin dynamics simulations to monitor the step-by-step movement of DNA through different mutations of α-hemolysin protein nanopores. We found that although the average translocation time per nucleotide is longer, in agreement with experiments, the DNA nucleotides do not translocate with a uniform speed. Furthermore, the location and spacing of the charge decorations can alter the translocation dynamics significantly, trapping DNA in some cases. Our findings can give insights when designing charge patterns in nanopores.
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Affiliation(s)
- Ining Jou
- Department of Polymer Science and Engineering, Conte Research Center, University of Massachusetts, Amherst, Massachusetts
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, Conte Research Center, University of Massachusetts, Amherst, Massachusetts.
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Wells CC, Melnikov DV, Gracheva ME. Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore. J Chem Phys 2017; 147:054903. [PMID: 28789548 DOI: 10.1063/1.4995423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.
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Affiliation(s)
- Craig C Wells
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
| | - Dmitriy V Melnikov
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
| | - Maria E Gracheva
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
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32
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Laszlo AH, Derrrington IM, Gundlach JH. Subangstrom Measurements of Enzyme Function Using a Biological Nanopore, SPRNT. Methods Enzymol 2016; 582:387-414. [PMID: 28062043 DOI: 10.1016/bs.mie.2016.09.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nanopores are emerging as new single-molecule tools in the study of enzymes. Based on the progress in nanopore sequencing of DNA, a tool called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT) was developed to measure the movement of enzymes along DNA in real time. In this new method, an enzyme is loaded onto a DNA (or RNA) molecule. A single-stranded DNA end of this complex is drawn into a nanopore by an electrostatic potential that is applied across the pore. The single-stranded DNA passes through the pore's constriction until the enzyme comes into contact with the pore. Further progression of the DNA through the pore is then controlled by the enzyme. An ion current that flows through the pore's constriction is modulated by the DNA in the constriction. Analysis of ion current changes reveals the advance of the DNA with high spatiotemporal precision, thereby providing a real-time record of the enzyme's activity. Using an engineered version of the protein nanopore MspA, SPRNT has spatial resolution as small as 40pm at millisecond timescales, while simultaneously providing the DNA's sequence within the enzyme. In this chapter, SPRNT is introduced and its extraordinary potential is exemplified using the helicase Hel308. Two distinct substates are observed for each one-nucleotide advance; one of these about half-nucleotide long steps is ATP dependent and the other is ATP independent. The spatiotemporal resolution of this low-cost single-molecule technique lifts the study of enzymes to a new level of precision, enabling exploration of hitherto unobservable enzyme dynamics in real time.
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Affiliation(s)
- A H Laszlo
- University of Washington, Seattle, WA, United States
| | | | - J H Gundlach
- University of Washington, Seattle, WA, United States.
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33
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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34
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Wloka C, Mutter NL, Soskine M, Maglia G. Alpha-Helical Fragaceatoxin C Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic Acid Analysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carsten Wloka
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Natalie Lisa Mutter
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Misha Soskine
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Giovanni Maglia
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
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35
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Wloka C, Mutter NL, Soskine M, Maglia G. Alpha-Helical Fragaceatoxin C Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic Acid Analysis. Angew Chem Int Ed Engl 2016; 55:12494-8. [DOI: 10.1002/anie.201606742] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Carsten Wloka
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Natalie Lisa Mutter
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Misha Soskine
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Giovanni Maglia
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
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36
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Manara RMA, Guy AT, Wallace EJ, Khalid S. Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin. J Chem Theory Comput 2016; 11:810-6. [PMID: 26579606 DOI: 10.1021/ct501081h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Next generation DNA sequencing methods that utilize protein nanopores have the potential to revolutionize this area of biotechnology. While the technique is underpinned by simple physics, the wild-type protein pores do not have all of the desired properties for efficient and accurate DNA sequencing. Much of the research efforts have focused on protein nanopores, such as α-hemolysin from Staphylococcus aureus. However, the speed of DNA translocation has historically been an issue, hampered in part by incomplete knowledge of the energetics of translocation. Here we have utilized atomistic molecular dynamics simulations of nucleotide fragments in order to calculate the potential of mean force (PMF) through α-hemolysin. Our results reveal specific regions within the pore that play a key role in the interaction with DNA. In particular, charged residues such as D127 and K131 provide stabilizing interactions with the anionic DNA and therefore are likely to reduce the speed of translocation. These regions provide rational targets for pore optimization. Furthermore, we show that the energetic contributions to the protein-DNA interactions are a complex combination of electrostatics and short-range interactions, often mediated by water molecules.
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Affiliation(s)
- Richard M A Manara
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Andrew T Guy
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - E Jayne Wallace
- Oxford Nanopore Technologies Ltd., Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, United Kingdom
| | - Syma Khalid
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton , Southampton SO17 1BJ, United Kingdom
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37
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De Biase PM, Ervin EN, Pal P, Samoylova O, Markosyan S, Keehan MG, Barrall GA, Noskov SY. What controls open-pore and residual currents in the first sensing zone of alpha-hemolysin nanopore? Combined experimental and theoretical study. NANOSCALE 2016; 8:11571-11579. [PMID: 27210516 DOI: 10.1039/c6nr00164e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The electrophoretic transport of single-stranded DNA through biological nanopores such as alpha-hemolysin (αHL) is a promising and cost-effective technology with the potential to revolutionize genomics. The rational design of pores with the controlled polymer translocation rates and high contrast between different nucleotides could improve significantly nanopore sequencing applications. Here, we apply a combination of theoretical and experimental methods in an attempt to elucidate several selective modifications in the pore which were proposed to be central for the effective discrimination between purines and pyrimidines. Our nanopore test set includes the wild type αHL and six mutants (E111N/M113X/K147N) in which the cross-section and chemical functionality of the first constriction zone of the pore are modified. Electrophysiological recordings were combined with all-atom Molecular Dynamics simulations (MD) and a recently developed Brownian Dynamics (BROMOC) protocol to investigate residual ion currents and pore-DNA interactions for two homo-polymers e.g. poly(dA)40 or poly(dC)40 blocking the pore. The calculated residual currents and contrast in the poly(dA)40/poly(dC)40 blocked pore are in qualitative agreement with the experimental recordings. We showed that a simple structural metric allows rationalization of key elements in the emergent contrast between purines and pyrimidines in the modified αHL mutants. The shape of the pore and its capacity for hydrogen bonding to a translocated polynucleotide are two essential parameters for contrast optimization. To further probe the impact of these two factors in the ssDNA sensing, we eliminated the effect of the primary constriction using serine substitutions (i.e. E111S/M113S/T145S/K147S) and increased the hydrophobic volume of the central residue in the secondary constriction (L135I). This pore modification sharply increased the contrast between Adenine (A) and Cytosine (C).
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Affiliation(s)
- Pablo M De Biase
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB T2N 2N4, Canada.
| | - Eric N Ervin
- Electronic BioSciences, 5754 Pacific Center Blvd., Ste. 204, San Diego, CA 92121, USA.
| | - Prithwish Pal
- Electronic BioSciences, 5754 Pacific Center Blvd., Ste. 204, San Diego, CA 92121, USA.
| | - Olga Samoylova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB T2N 2N4, Canada.
| | - Suren Markosyan
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB T2N 2N4, Canada.
| | - Michael G Keehan
- Electronic BioSciences, 5754 Pacific Center Blvd., Ste. 204, San Diego, CA 92121, USA.
| | - Geoffrey A Barrall
- Electronic BioSciences, 5754 Pacific Center Blvd., Ste. 204, San Diego, CA 92121, USA.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB T2N 2N4, Canada.
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38
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Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. NANOSCALE 2016; 8:9600-13. [PMID: 27103233 PMCID: PMC4860951 DOI: 10.1039/c6nr01061j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.
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Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, P-213 Mosier Hall, 1800 Denison Ave, Manhattan, Kansas, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W Green St, Urbana, IL, USA.
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39
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Bhattacharya S, Yoo J, Aksimentiev A. Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore. ACS NANO 2016; 10:4644-51. [PMID: 27054820 PMCID: PMC4849127 DOI: 10.1021/acsnano.6b00940] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing via measurement of ionic current blockades possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. Unexpectedly, we find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout.
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Affiliation(s)
- Swati Bhattacharya
- Department of Physics, University of Illinois at Urbana{Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Jejoong Yoo
- Department of Physics, University of Illinois at Urbana{Champaign, 1110 West Green Street, Urbana, Illinois 61801
- Center for the Physics of Living Cells
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana{Champaign, 1110 West Green Street, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Technology
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40
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Laszlo AH, Derrington IM, Gundlach JH. MspA nanopore as a single-molecule tool: From sequencing to SPRNT. Methods 2016; 105:75-89. [PMID: 27045943 PMCID: PMC4967004 DOI: 10.1016/j.ymeth.2016.03.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/10/2016] [Accepted: 03/29/2016] [Indexed: 11/15/2022] Open
Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a new tool for analyzing the motion of nucleic acids through molecular motors. With SPRNT, individual enzymatic motions along DNA as small as 40 pm can be resolved on sub-millisecond time scales. Additionally, SPRNT reveals an enzyme’s exact location with respect to a DNA strand’s nucleotide sequence, enabling identification of sequence-specific behaviors. SPRNT is enabled by a mutant version of the biological nanopore formed by Mycobacterium smegmatis porin A (MspA). SPRNT is strongly rooted in nanopore sequencing and therefore requires a solid understanding of basic principles of nanopore sequencing. Furthermore, SPRNT shares tools developed for nanopore sequencing and extends them to analysis of single-molecule kinetics. As such, this review begins with a brief history of our work developing the nanopore MspA for nanopore sequencing. We then describe the underlying principles of SPRNT, how it works in detail, and propose some potential future uses. We close with a comparison of SPRNT to other techniques and we present the methods that will enable others to use SPRNT.
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Affiliation(s)
- Andrew H Laszlo
- University of Washington, Department of Physics, 3910 15th Ave NE, Seattle, WA 98195, USA
| | - Ian M Derrington
- University of Washington, Department of Physics, 3910 15th Ave NE, Seattle, WA 98195, USA
| | - Jens H Gundlach
- University of Washington, Department of Physics, 3910 15th Ave NE, Seattle, WA 98195, USA.
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41
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Friedrich SM, Zec HC, Wang TH. Analysis of single nucleic acid molecules in micro- and nano-fluidics. LAB ON A CHIP 2016; 16:790-811. [PMID: 26818700 PMCID: PMC4767527 DOI: 10.1039/c5lc01294e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.
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Affiliation(s)
- Sarah M Friedrich
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Helena C Zec
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA. and Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
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42
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Ding Y, Fleming AM, White HS, Burrows CJ. Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin. ACS NANO 2015; 9:11325-32. [PMID: 26506108 PMCID: PMC4876701 DOI: 10.1021/acsnano.5b05055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The α-hemolysin (α-HL) nanopore can detect DNA strands under an electrophoretic force via many regions of the channel. Our laboratories previously demonstrated that trapping duplex DNA in the vestibule of wild-type α-HL under force could distinguish the presence of an abasic site compared to a G:C base pair positioned in the latch zone at the top of the vestibule. Herein, a series of duplexes were probed in the latch zone to establish if this region can detect more subtle features of base pairs beyond the complete absence of a base. The results of these studies demonstrate that the most sensitive region of the latch can readily discriminate duplexes in which one G:C base pair is replaced by an A:T. Additional experiments determined that while neither 8-oxo-7,8-dihydroguanine nor 7-deazaguanine opposite C could be differentiated from a G:C base pair, in contrast, the epigenetic marker 5-methylcytosine, when present in both strands of the duplex, yielded new blocking currents when compared to strands with unmodified cytosine. The results are discussed with respect to experimental design for utilization of the latch zone of α-HL to probe specific regions of genomic samples.
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Affiliation(s)
| | | | - Henry S. White
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
| | - Cynthia J. Burrows
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
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43
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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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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45
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Abstract
The α-hemolysin (αHL) protein nanopore has been investigated previously as a base detector for the strand sequencing of DNA and RNA. Recent findings have suggested that shorter pores might provide improved base discrimination. New work has also shown that truncated-barrel mutants (TBM) of αHL form functional pores in lipid bilayers. Therefore, we tested TBM pores for the ability to recognize bases in DNA strands immobilized within them. In the case of TBMΔ6, in which the barrel is shortened by ∼16 Å, one of the three recognition sites found in the wild-type pore, R1, was almost eliminated. With further mutagenesis (Met113 → Gly), R1 was completely removed, demonstrating that TBM pores can mediate sharpened recognition. Remarkably, a second mutant of TBMΔ6 (Met113 → Phe) was able to bind the positively charged β-cyclodextrin, am7βCD, unusually tightly, permitting the continuous recognition of individual nucleoside monophosphates, which would be required for exonuclease sequencing mediated by nanopore base identification.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | | | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
- Corresponding Author:
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46
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DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants. Sci Rep 2015; 5:12783. [PMID: 26255609 PMCID: PMC4530457 DOI: 10.1038/srep12783] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/30/2015] [Indexed: 11/24/2022] Open
Abstract
MspA has been identified as a promising candidate protein as a component of a nanopore-based DNA-sequencing device. However the wildtype protein must be engineered to incorporate all of the features desirable for an accurate and efficient device. In the present study we have utilized atomistic molecular dynamics to perform umbrella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation of the four DNA nucleotides through MspA. We show there is an energetic barrier to translocation of individual nucleotides through a mutant that closely resembles the wildtype protein, but not through a mutant engineered for the purpose of sequencing. Crucially we are able to quantify the change in free energy for mutating key residues. Thus providing a quantitative characterisation of the energetic impact of individual amino acid sidechains on nucleotide translocation through the pore of MspA.
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47
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Hadi-Alijanvand S, Mobasheri H, Hadi-Alijanvand H. Application of OmpF nanochannel forming protein in polynucleotide sequence recognition. J Mol Recognit 2015; 27:575-87. [PMID: 25178853 DOI: 10.1002/jmr.2381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/31/2014] [Accepted: 04/09/2014] [Indexed: 01/09/2023]
Abstract
Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
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Affiliation(s)
- Saeid Hadi-Alijanvand
- Laboratory of Membrane Biophysics and Macromolecules, Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran
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48
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Hadi-Alijanvand H, Rouhani M. Journey of poly-nucleotides through OmpF porin. J Phys Chem B 2015; 119:6113-28. [PMID: 25965338 DOI: 10.1021/acs.jpcb.5b00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.
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Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Maryam Rouhani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
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49
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Johnson RP, Fleming AM, Jin Q, Burrows CJ, White HS. Temperature and electrolyte optimization of the α-hemolysin latch sensing zone for detection of base modification in double-stranded DNA. Biophys J 2015; 107:924-31. [PMID: 25140427 DOI: 10.1016/j.bpj.2014.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/16/2014] [Accepted: 07/03/2014] [Indexed: 01/24/2023] Open
Abstract
The latch region of the wild-type protein pore α-hemolysin (α-HL) constitutes a sensing zone for individual abasic sites (and furan analogs) in double-stranded DNA (dsDNA). The presence of an abasic site or furan within a DNA duplex, electrophoretically captured in the α-HL vestibule and positioned at the latch region, can be detected based on the current blockage prior to duplex unzipping. We investigated variations in blockage current as a function of temperature (12-35°C) and KCl concentration (0.15-1.0 M) to understand the origin of the current signature and to optimize conditions for identifying the base modification. In 1 M KCl solution, substitution of a furan for a cytosine base in the latch region results in an ∼ 8 kJ mol(-1) decrease in the activation energy for ion transport through the protein pore. This corresponds to a readily measured ∼ 2 pA increase in current at room temperature. Optimal resolution for detecting the presence of a furan in the latch region is achieved at lower KCl concentrations, where the noise in the measured blockage current is significantly lower. The noise associated with the blockage current also depends on the stability of the duplex (as measured from the melting temperature), where a greater noise in the measured blockage current is observed for less stable duplexes.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Qian Jin
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
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50
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Stoddart D, Franceschini L, Heron A, Bayley H, Maglia G. DNA stretching and optimization of nucleobase recognition in enzymatic nanopore sequencing. NANOTECHNOLOGY 2015; 26:084002. [PMID: 25648138 PMCID: PMC4410315 DOI: 10.1088/0957-4484/26/8/084002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In nanopore sequencing, where single DNA strands are electrophoretically translocated through a nanopore and the resulting ionic signal is used to identify the four DNA bases, an enzyme has been used to ratchet the nucleic acid stepwise through the pore at a controlled speed. In this work, we investigated the ability of alpha-hemolysin nanopores to distinguish the four DNA bases under conditions that are compatible with the activity of DNA-handling enzymes. Our findings suggest that in immobilized strands, the applied potential exerts a force on DNA (∼10 pN at +160 mV) that increases the distance between nucleobases by about 2.2 Å V(-1). The four nucleobases can be resolved over wide ranges of applied potentials (from +60 to +220 mV in 1 m KCl) and ionic strengths (from 200 mM KCl to 1 M KCl at +160 mV) and nucleobase recognition can be improved when the ionic strength on the side of the DNA-handling enzyme is low, while the ionic strength on the opposite side is high.
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Affiliation(s)
- David Stoddart
- University of Oxford, Chemistry Research Laboratory, Oxford, UK
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