1
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Lin Y, Liang R, Xie K, Ma T, Zhang J, Xu T, Wang A, Liu S. Puerarin inhibits cisplatin-induced ototoxicity in mice through regulation of TRPV1-dependent calcium overload. Biochem Pharmacol 2024; 220:115962. [PMID: 38043717 DOI: 10.1016/j.bcp.2023.115962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023]
Abstract
Puerarin (PUE), a flavonoid derivative with vasodilatory effects found in the traditional Chinese medicine kudzu, has anti-sensorineural hearing loss properties. However, the mechanism of its protective effect against ototoxicity is not well understood. In this study, we used in vitro and in vivo methods to investigate the protective mechanism of puerarin against cisplatin (CDDP)-induced ototoxicity. We established an ototoxicity model of CDDP in BALB/c mice and assessed the degree of hearing loss and cochlear cell damage. We used bioinformatics analysis, molecular docking, histological analysis, and biochemical and molecular biology to detect the expression of relevant factors. Our results show that puerarin improved CDDP-induced hearing loss and reduced hair cell loss. It also blocked CDDP-induced activation of TRPV1 and inhibited activation of IP3R1 to prevent intracellular calcium overload. Additionally, puerarin blocked CDDP-stimulated p65 activation, reduced excessive ROS production, and alleviated cochlear cell apoptosis. Our study provides new evidence and potential targets for the protective effect of puerarin against drug-induced hearing loss. Puerarin ameliorates cisplatin-induced ototoxicity and blocks cellular apoptosis by inhibiting CDDP activated TRPV1/IP3R1/p65 pathway, blocking induction of calcium overload and excessive ROS expression.
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Affiliation(s)
- Yuhan Lin
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Rui Liang
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Kairong Xie
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Tingting Ma
- Life Science Institute, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Jigui Zhang
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Tao Xu
- Life Science Institute, Jinzhou Medical University, Jinzhou 121000 PR China
| | - Aimei Wang
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China.
| | - Shuangyue Liu
- Department of Physiology, Jinzhou Medical University, Jinzhou 121000 PR China.
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2
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Xia B, Fang J, Ma S, Ma M, Yao G, Li T, Cheng X, Wen L, Gao Z. Mapping the Acetylamino and Carboxyl Groups on Glycans by Engineered α-Hemolysin Nanopores. J Am Chem Soc 2023; 145:18812-18824. [PMID: 37527445 DOI: 10.1021/jacs.3c03563] [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] [Indexed: 08/03/2023]
Abstract
Glycan is a crucial class of biological macromolecules with important biological functions. Functional groups determine the chemical properties of glycans, which further affect their biological activities. However, the structural complexity of glycans has set a technical hurdle for their direct identification. Nanopores have emerged as highly sensitive biosensors that are capable of detecting and characterizing various analytes. Here, we identified the functional groups on glycans with a designed α-hemolysin nanopore containing arginine mutations (M113R), which is specifically sensitive to glycans with acetamido and carboxyl groups. Molecular dynamics simulations indicated that the acetamido and carboxyl groups of the glycans produce unique electrical signatures by forming polar and electrostatic interactions with the M113R nanopores. Using these electrical features as the fingerprints, we mapped the length of the glycans containing acetamido and carboxyl groups at the monosaccharide, disaccharide, and trisaccharide levels. This proof-of-concept study provides a promising foundation for developing single-molecule glycan fingerprinting libraries and demonstrates the capability of biological nanopores in glycan sequencing.
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Affiliation(s)
- Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Shengzhou Ma
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mengyao Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Lingang Laboratory, School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Tiehai Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, China
| | - Liuqing Wen
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
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3
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Chen X, Zhao X, Ma R, Hu Y, Cui C, Mi Z, Dou R, Pan D, Shan X, Wang L, Fan C, Lu X. Ionic Current Fluctuation and Orientation of Tetrahedral DNA Nanostructures in a Solid-State Nanopore. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107237. [PMID: 35092143 DOI: 10.1002/smll.202107237] [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: 11/22/2021] [Revised: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Understanding the dynamic behavior of a nanostructure translocating through a nanopore is important for various applications. In this paper, the characteristics in ion current traces of tetrahedral DNA nanostructures (TDN) translocating through a solid-state nanopore are examined, by combined experimental and theoretical simulations. The results of finite element analysis reveal the correlation between orientation of TDN and the conductance blockade. The experimentally measured fluctuations in the conductance blockade, expressed as voltage-dependent histogram profiles, are consistent with the simulation, revealing the nature of a random distribution in orientation and weak influence of electrostatic and viscous torques. The step changes in orientation of a TDN during translocation are further explained by the collision with the nanopore, while the gradual changes in orientation illustrate the impact of a weak torque field in the nano-fluidic channel. The results demonstrate a general method and basic understanding in the dynamic behavior of nanostructures translocating through solid-state nanopores.
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Affiliation(s)
- Xiaoyu Chen
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xinjia Zhao
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ruiping Ma
- Beijing Normal University, Beijing, 100088, China
| | - Ying Hu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengjun Cui
- Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
| | - Zhuang Mi
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ruifen Dou
- Beijing Normal University, Beijing, 100088, China
| | - Dun Pan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University Shanghai, Shanghai, 200030, China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lihua Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinghua Lu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
- Center for Excellence in Topological Quantum Computation, Beijing, 100190, China
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4
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Ben Khedher M, Ghedira K, Rolain JM, Ruimy R, Croce O. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. Int J Mol Sci 2022; 23:1395. [PMID: 35163319 PMCID: PMC8835973 DOI: 10.3390/ijms23031395] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.
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Affiliation(s)
- Mariem Ben Khedher
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis 1002, Tunisia;
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
| | - Raymond Ruimy
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM, Université Côte D’Azur, 06108 Nice, France
| | - Olivier Croce
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
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5
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Mohammadi MM, Bavi O. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophys Rev 2021; 14:99-110. [PMID: 34840616 PMCID: PMC8609259 DOI: 10.1007/s12551-021-00857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.
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Affiliation(s)
- Mohammad M Mohammadi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
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6
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Wen C, Dematties D, Zhang SL. A Guide to Signal Processing Algorithms for Nanopore Sensors. ACS Sens 2021; 6:3536-3555. [PMID: 34601866 PMCID: PMC8546757 DOI: 10.1021/acssensors.1c01618] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/19/2022]
Abstract
Nanopore technology holds great promise for a wide range of applications such as biomedical sensing, chemical detection, desalination, and energy conversion. For sensing performed in electrolytes in particular, abundant information about the translocating analytes is hidden in the fluctuating monitoring ionic current contributed from interactions between the analytes and the nanopore. Such ionic currents are inevitably affected by noise; hence, signal processing is an inseparable component of sensing in order to identify the hidden features in the signals and to analyze them. This Guide starts from untangling the signal processing flow and categorizing the various algorithms developed to extracting the useful information. By sorting the algorithms under Machine Learning (ML)-based versus non-ML-based, their underlying architectures and properties are systematically evaluated. For each category, the development tactics and features of the algorithms with implementation examples are discussed by referring to their common signal processing flow graphically summarized in a chart and by highlighting their key issues tabulated for clear comparison. How to get started with building up an ML-based algorithm is subsequently presented. The specific properties of the ML-based algorithms are then discussed in terms of learning strategy, performance evaluation, experimental repeatability and reliability, data preparation, and data utilization strategy. This Guide is concluded by outlining strategies and considerations for prospect algorithms.
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Affiliation(s)
- Chenyu Wen
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Dario Dematties
- Instituto
de Ciencias Humanas, Sociales y Ambientales, CONICET Mendoza Technological Scientific Center, Mendoza M5500, Argentina
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
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7
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Choi J, Jia Z, Riahipour R, McKinney CJ, Amarasekara CA, Weerakoon-Ratnayake KM, Soper SA, Park S. Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102567. [PMID: 34558175 PMCID: PMC8542607 DOI: 10.1002/smll.202102567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label-free detection of the nucleotides to determine their electrophoretic mobility (i.e., time-of-flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2-deoxyribonucleoside 5'-monophosphates, dNMPs, molecules in a label-free manner by nanoscale electrophoresis. This is made possible by positioning two sub-10 nm in-plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label-free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in-plane nanopores and integrating different pre- and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication.
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Affiliation(s)
- Junseo Choi
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Zheng Jia
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Ramin Riahipour
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Collin J. McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Charuni A. Amarasekara
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Kumuditha M. Weerakoon-Ratnayake
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, University of Kansas, Lawrence, KS 66047, USA
- Department of Kansas Biology and KUCC, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sunggook Park
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of Bio-Modular Multiscale Systems for Precision Medicine, USA
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8
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Niedzwiecki DJ, Chou YC, Xia Z, Thei F, Drndić M. Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:031301. [PMID: 32259993 DOI: 10.1063/1.5138210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.
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Affiliation(s)
- David J Niedzwiecki
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Yung-Chien Chou
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
| | - Zehui Xia
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Federico Thei
- Elements, SRL, Viale G. Marconi 438, Cesena 47521, Italy
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
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9
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Carabeo-Pérez A, Guerra-Rivera G, Ramos-Leal M, Jiménez-Hernández J. Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems. Appl Microbiol Biotechnol 2019; 103:9379-9390. [PMID: 31420693 DOI: 10.1007/s00253-019-10052-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/17/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
Abstract
Microbial metagenome analysis has proven its usefulness to investigate the microbiomes present in technical engineered ecosystems such as anaerobic digestion systems. The analysis of the total microbial genomic DNA allows the detailed determination of both the microbial community structure and its functionality. In addition, it enables to study the response of the microbiome to alterations in technical process parameters. Strategies of functional microbial networks to face abiotic stressors, e.g., resistance, resilience, and reorganization, can be evaluated with respect to overall process optimization. The objective of this paper is to review the main metagenomic tools used for effective studies on anaerobic digestion systems in monitoring the dynamic of the microbiomes, as well as the factors that have been identified so far as limiting the metagenomic studies in this ecosystems.
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Affiliation(s)
- Annerys Carabeo-Pérez
- Centro de Estudios de Energía y Procesos Industriales, Universidad de Sancti Spíritus "José Martí Pérez", Ave de los Mártires No. 360, CP 60100, Sancti Spíritus, Cuba
| | - Gilda Guerra-Rivera
- Facultad de Biología, Universidad de La Habana, Calle 25 e/ I y J, Vedado, CP 10400, Havana, Cuba
| | - Miguel Ramos-Leal
- Instituto de investigaciones de fruticultura tropical, Ave. 7ma No. 3005, et. 30 y 32, Playa, CP 11300, Havana, Cuba
| | - Janet Jiménez-Hernández
- Centro de Estudios de Energía y Procesos Industriales, Universidad de Sancti Spíritus "José Martí Pérez", Ave de los Mártires No. 360, CP 60100, Sancti Spíritus, Cuba.
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10
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Alidoosti E, Zhao H. The effects of electrostatic correlations on the ionic current rectification in conical nanopores. Electrophoresis 2019; 40:2655-2661. [PMID: 31206777 DOI: 10.1002/elps.201900127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 11/08/2022]
Abstract
Ion-ion electrostatic correlations are recognized to play a significant role in the presence of concentrated multivalent electrolytes. To account for their impact on ionic current rectification phenomenon in conical nanopores, we use the modified continuum Poisson-Nernst-Planck (PNP) equations by Bazant et al. Coupled with the Stokes equations, the effects of the EOF are also included. We thoroughly investigate the dependence of the ionic current rectification ratios as a function of the double layer thickness and the electrostatic correlation length. By considering the electrostatic correlations, the modified PNP model successfully captures the ionic current rectification reversal in nanopores filled with lanthanum chloride LaCl3 . This finding qualitatively agrees with the experimental observations that cannot be explained by the standard PNP model, suggesting that ion-ion electrostatic correlations are responsible for this reversal behavior. The modified PNP model not only can be used to explain the experiments, but also go beyond to provide a design tool for nanopore applications involving multivalent electrolytes.
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Affiliation(s)
- Elaheh Alidoosti
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, USA
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, USA
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11
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Athreya NBM, Sarathy A, Leburton JP. Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems. ACS Sens 2018; 3:1032-1039. [PMID: 29663800 DOI: 10.1021/acssensors.8b00192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a scalable device design of a dense array of multiple nanopores made from nanoscale semiconductor materials to detect and identify translocations of many biomolecules in a massively parallel detection scheme. We use molecular dynamics coupled to nanoscale device simulations to illustrate the ability of this device setup to uniquely identify DNA parallel translocations. We show that the transverse sheet currents along membranes are immune to the crosstalk effects arising from simultaneous translocations of biomolecules through multiple pores, due to their ability to sense only the local potential changes. We also show that electronic sensing across the nanopore membrane offers a higher detection resolution compared to ionic current blocking technique in a multipore setup, irrespective of the irregularities that occur while fabricating the nanopores in a two-dimensional membrane.
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12
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Wang Y, Tian K, Du X, Shi RC, Gu LQ. Remote Activation of a Nanopore for High-Performance Genetic Detection Using a pH Taxis-Mimicking Mechanism. Anal Chem 2017; 89:13039-13043. [PMID: 29183111 PMCID: PMC6174115 DOI: 10.1021/acs.analchem.7b03979] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerolysin protein pore has been widely used for sensing peptides and proteins. However, only a few groups explored this nanopore for nucleic acids detection. The challenge is the extremely low capture efficiency for nucleic acids (>10 bases), which severely lowers the sensitivity of an aerolysin-based genetic biosensor. Here we reported a simple and easy-to-operate approach to noncovalently transform aerolysin into a highly nucleic acids-sensitive nanopore. Through a remote pH-modulation mechanism, we simply lower the pH on one side of the pore, then aerolysin is immediately "activated" and enabled to capture target DNA/RNA efficiently from the opposite side of the pore. This mechanism also decelerates DNA translocation, a desired property for sequencing and gene detection, allowing temporal separation of DNAs in different lengths. This method provides insight into the nanopore engineering for biosensing, making aerolysin applicable in genetic and epigenetic detections of long nucleic acids.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiao Du
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Rui-Cheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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13
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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14
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Vu T, Davidson SL, Borgesi J, Maksudul M, Jeon TJ, Shim J. Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers. RSC Adv 2017. [DOI: 10.1039/c7ra08063h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This mini-review paper is a comprehensive outline of nanopore technology applications in the detection and study of various cancer causal factors.
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Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Shanna-Leigh Davidson
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Julia Borgesi
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Mowla Maksudul
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Tae-Joon Jeon
- Department of Biological Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Jiwook Shim
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
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15
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Youell J, Sikora AE, Vejsadová Š, Weiserova M, Smith JR, Firman K. Cofactor induced dissociation of the multifunctional multisubunit EcoR124I investigated using electromobility shift assays, AFM and SPR. RSC Adv 2017. [DOI: 10.1039/c7ra07505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have applied three techniques to the study of subunit assembly of the Type IC Restriction–Modification enzyme EcoR124I.
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Affiliation(s)
- James Youell
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Aneta E. Sikora
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Štěpánka Vejsadová
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
| | - Marie Weiserova
- Institute of Microbiology
- ASCR, v.v.i
- 142 20 Prague 4
- Czech Republic
| | - James R. Smith
- School of Pharmacy and Biomedical Sciences
- University of Portsmouth
- Portsmouth PO1 2DT
- UK
| | - Keith Firman
- School of Biological Sciences
- University of Portsmouth
- Portsmouth PO1 2DY
- UK
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16
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Cherukuri Y, Janga SC. Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches. BMC Genomics 2016; 17 Suppl 7:507. [PMID: 27556636 PMCID: PMC5001211 DOI: 10.1186/s12864-016-2895-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Improved DNA sequencing methods have transformed the field of genomics over the last decade. This has become possible due to the development of inexpensive short read sequencing technologies which have now resulted in three generations of sequencing platforms. More recently, a new fourth generation of Nanopore based single molecule sequencing technology, was developed based on MinION® sequencer which is portable, inexpensive and fast. It is capable of generating reads of length greater than 100 kb. Though it has many specific advantages, the two major limitations of the MinION reads are high error rates and the need for the development of downstream pipelines. The algorithms for error correction have already emerged, while development of pipelines is still at nascent stage. Results In this study, we benchmarked available assembler algorithms to find an appropriate framework that can efficiently assemble Nanopore sequenced reads. To address this, we employed genome-scale Nanopore sequenced datasets available for E. coli and yeast genomes respectively. In order to comprehensively evaluate multiple algorithmic frameworks, we included assemblers based on de Bruijn graphs (Velvet and ABySS), Overlap Layout Consensus (OLC) (Celera) and Greedy extension (SSAKE) approaches. We analyzed the quality, accuracy of the assemblies as well as the computational performance of each of the assemblers included in our benchmark. Our analysis unveiled that OLC-based algorithm, Celera, could generate a high quality assembly with ten times higher N50 & mean contig values as well as one-fifth the number of total number of contigs compared to other tools. Celera was also found to exhibit an average genome coverage of 12 % in E. coli dataset and 70 % in Yeast dataset as well as relatively lesser run times. In contrast, de Bruijn graph based assemblers Velvet and ABySS generated the assemblies of moderate quality, in less time when there is no limitation on the memory allocation, while greedy extension based algorithm SSAKE generated an assembly of very poor quality but with genome coverage of 90 % on yeast dataset. Conclusion OLC can be considered as a favorable algorithmic framework for the development of assembler tools for Nanopore-based data, followed by de Bruijn based algorithms as they consume relatively less or similar run times as OLC-based algorithms for generating assembly, irrespective of the memory allocated for the task. However, few improvements must be made to the existing de Bruijn implementations in order to generate an assembly with reasonable quality. Our findings should help in stimulating the development of novel assemblers for handling Nanopore sequence data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2895-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yesesri Cherukuri
- Department of Bio Health Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IA, 46202, USA
| | - Sarath Chandra Janga
- Department of Bio Health Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IA, 46202, USA. .,Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IA, 46202, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IA, 46202, USA.
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17
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Liang L, Shen JW, Zhang Z, Wang Q. DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments. Biosens Bioelectron 2015; 89:280-292. [PMID: 26711358 DOI: 10.1016/j.bios.2015.12.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, two-dimensional (2D) materials (mainly including graphene, boron nitride, MoS2 etc.) have stimulated exploding interests in sensor applications. 2D-material based nanoscale DNA sequencing is a single-molecule technique with revolutionary potential. In this paper, we review the methodology of DNA sequencing based on the measurements of ionic current, force peak, and transverse electrical currents etc. by 2D materials. The advantages and disadvantages of DNA sequencing by 2D materials are discussed. Besides the recent development of experiments, we will focus on the theoretical calculations of DNA sequencing, which have been played a critical role in the development of this field. Special emphasis will focus on the disagreements between experiments and theoretical calculations, and the explanations for the discrepancy will be highlighted. Finally, some new plausible sequencing methods from computational studies will be discussed, which may be applied in the realistic DNA sequencing experiments in future.
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Affiliation(s)
- Lijun Liang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Zhisen Zhang
- Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, Xiamen 361005, People' s Republic of China
| | - Qi Wang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
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18
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Xia K, Novak BR, Weerakoon-Ratnayake KM, Soper SA, Nikitopoulos DE, Moldovan D. Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study. J Phys Chem B 2015; 119:11443-58. [PMID: 26237155 DOI: 10.1021/acs.jpcb.5b02798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide-wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide-wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide-wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.
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Affiliation(s)
- Kai Xia
- Department of Mechanical and Industrial Engineering, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Brian R Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Kumuditha M Weerakoon-Ratnayake
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States.,Department of Biomedical Engineering, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Steven A Soper
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599, Unites States.,Department of Biomedical Engineering, University of North Carolina , Chapel Hill, North Carolina 27599, United States.,Department of Biomedical Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Dimitris E Nikitopoulos
- Department of Mechanical and Industrial Engineering, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Dorel Moldovan
- Department of Mechanical and Industrial Engineering, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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19
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Ui M, Harima K, Takei T, Tsumoto K, Tabata KV, Noji H, Endo S, Akiyama K, Muraoka T, Kinbara K. Grafting synthetic transmembrane units to the engineered low-toxicity α-hemolysin to restore its hemolytic activity. MOLECULAR BIOSYSTEMS 2015; 10:3199-206. [PMID: 25267196 DOI: 10.1039/c4mb00405a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The chemical modification of proteins to provide desirable functions and/or structures broadens their possibilities for use in various applications. Usually, proteins can acquire new functions and characteristics, in addition to their original ones, via the introduction of synthetic functional moieties. Here, we adopted a more radical approach to protein modification, i.e., the replacement of a functional domain of proteins with alternative chemical compounds to build "cyborg proteins." As a proof of concept model, we chose staphylococcal α-hemolysin (Hla), which is a well-studied, pore-forming toxin. The hemolytic activity of Hla mutants was dramatically decreased by truncation of the stem domain, which forms a β-barrel pore in the membrane. However, the impaired hemolytic activity was significantly restored by attaching a pyrenyl-maleimide unit to the cysteine residue that was introduced in the remaining stem domain. In contrast, negatively charged fluorescein-maleimide completely abolished the remaining activity of the mutants.
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Affiliation(s)
- Mihoko Ui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan.
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20
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Kremkow BG, Lee KH. Sequencing technologies for animal cell culture research. Biotechnol Lett 2014; 37:55-65. [DOI: 10.1007/s10529-014-1660-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/27/2014] [Indexed: 01/16/2023]
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21
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Liang L, Wang Q, Agren H, Tu Y. Computational studies of DNA sequencing with solid-state nanopores: key issues and future prospects. Front Chem 2014; 2:5. [PMID: 24790974 PMCID: PMC3982512 DOI: 10.3389/fchem.2014.00005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/05/2014] [Indexed: 01/25/2023] Open
Abstract
Owing to the potential use for real personalized genome sequencing, DNA sequencing with solid-state nanopores has been investigated intensively in recent time. However, the area still confronts problems and challenges. In this work, we present a brief overview of computational studies of key issues in DNA sequencing with solid-state nanopores by addressing the progress made in the last few years. We also highlight future challenges and prospects for DNA sequencing using this technology.
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Affiliation(s)
- Lijun Liang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden ; Department of Chemistry and Soft Matter Research Center, Zhejiang University Hangzhou, China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University Hangzhou, China
| | - Hans Agren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
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22
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Yadav NK, Shukla P, Omer A, Pareek S, Singh RK. Next generation sequencing: potential and application in drug discovery. ScientificWorldJournal 2014; 2014:802437. [PMID: 24688432 PMCID: PMC3933208 DOI: 10.1155/2014/802437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/18/2013] [Indexed: 01/07/2023] Open
Abstract
The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes sequencing by synthesis-fluorescent in situ sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization along with sequencing by ligation, and nanopore technology. Great impacts of these methods can be seen for solving the genome related problems of plant and animal kingdom that will open the door of a new era of genomics. This may ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is expected to advance and make the drug discovery process more rapid.
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Affiliation(s)
- Navneet Kumar Yadav
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Pooja Shukla
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
| | - Ankur Omer
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
| | - Shruti Pareek
- Jaipur National University, Jaipur, Rajasthan 302017, India
| | - R. K. Singh
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
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23
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Next-generation sequencing technologies and their potential impact on CHO cell-based biomanufacturing. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.52] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Pizzolato N, Fiasconaro A, Adorno DP, Spagnolo B. Translocation dynamics of a short polymer driven by an oscillating force. J Chem Phys 2013; 138:054902. [PMID: 23406144 DOI: 10.1063/1.4789016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We study the translocation dynamics of a short polymer moving in a noisy environment and driven by an oscillating force. The dynamics is numerically investigated by solving a Langevin equation in a two-dimensional domain. We consider a phenomenological cubic potential with a metastable state to model the polymer-pore interaction and the entropic free energy barrier characterizing the translocation process. The mean first translocation time of the center of inertia of polymers shows a nonmonotonic behavior, with a minimum, as a function of the number of the monomers. The dependence of the mean translocation time on the polymer chain length shows a monotonically increasing behavior for high values of the number of monomers. Moreover, the translocation time shows a minimum as a function of the frequency of the oscillating forcing field for all the polymer lengths investigated. This finding represents the evidence of the resonant activation phenomenon in the dynamics of polymer translocation, whose occurrence is maintained for different values of the noise intensity.
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Affiliation(s)
- Nicola Pizzolato
- Dipartimento di Fisica e Chimica, Università di Palermo and CNISM, Viale delle Scienze edificio 18, I-90128 Palermo, Italy
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25
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Mao M, Ghosal S, Hu G. Hydrodynamic flow in the vicinity of a nanopore induced by an applied voltage. NANOTECHNOLOGY 2013; 24:245202. [PMID: 23689946 PMCID: PMC3738177 DOI: 10.1088/0957-4484/24/24/245202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Continuum simulation is employed to study ion transport and fluid flow through a nanopore in a solid-state membrane under an applied potential drop. The results show the existence of concentration polarization layers on the surfaces of the membrane. The nonuniformity of the ionic distribution gives rise to an electric pressure that drives vortical motion in the fluid. There is also a net hydrodynamic flow through the nanopore due to an asymmetry induced by the membrane surface charge. The qualitative behavior is similar to that observed in a previous study using molecular dynamic simulations. The current-voltage characteristics show some nonlinear features but are not greatly affected by the hydrodynamic flow in the parameter regime studied. In the limit of thin Debye layers, the electric resistance of the system can be characterized using an equivalent circuit with lumped parameters. Generation of vorticity can be understood qualitatively from elementary considerations of the Maxwell stresses. However, the flow strength is a strongly nonlinear function of the applied field. Combination of electrophoretic and hydrodynamic effects can lead to ion selectivity in terms of valences and this could have some practical applications in separations.
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Affiliation(s)
- Mao Mao
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA.
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26
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Wolna AH, Fleming AM, An N, He L, White HS, Burrows CJ. Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α-Hemolysin Ion Channel. Isr J Chem 2013; 53:417-430. [PMID: 24052667 PMCID: PMC3773884 DOI: 10.1002/ijch.201300022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nanopore technology holds high potential for next-generation DNA sequencing. This method operates by drawing an individual single-stranded DNA molecule through a nanoscale pore while monitoring the current deflections that occur as the DNA passes through. Individual current levels for the four DNA nucleotides have been established by immobilization of an end biotinylated strand in the pore in which the nucleotide of interest is suspended at the most sensitive region of the ion channel. Due to the inherent reactivity of the DNA bases, many modified nucleotides in the genome exist resulting from oxidative and UV insults, among others. Herein, the current levels for the common DNA damages 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), uridine (U), abasic sites (AP), thymine dimers (T=T), thymine glycol (Tg) and 5-iodocytosine (5-I-C) were assessed via immobilization experiments. In some cases, the current difference between the damaged and canonical nucleotides was not well resolved; therefore, we took advantage of the chemical reactivity of the new functional groups present to make amine adducts that shifted the current levels outside the range of the native nucleotides. Among adducts studied, only the 2-aminomethyl-18-crown-6 adduct was able to give a large current shift in the immobilization experiment, as well as to be observed in a translocation experiment. The results show potential in providing current level modulators for identification of some types of DNA damage. In principle, any DNA base modification that can be converted chemically or enzymatically to an abasic site could be identified in this way.
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Affiliation(s)
- Anna H. Wolna
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Aaron M. Fleming
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Na An
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Lidong He
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Henry S. White
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry University of Utah 315 S 1400 East Salt Lake City, UT 84112-0850
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27
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Novak BR, Moldovan D, Nikitopoulos DE, Soper SA. Distinguishing single DNA nucleotides based on their times of flight through nanoslits: a molecular dynamics simulation study. J Phys Chem B 2013; 117:3271-9. [PMID: 23461845 DOI: 10.1021/jp309486c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transport of single molecules in nanochannels or nanoslits might be used to identify them via their transit (flight) times. In this paper, we present molecular dynamics simulations of transport of single deoxynucleotide 5'-monophoshates (dNMP) in aqueous solution under pressure-driven flow, to average velocities between 0.4 and 1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulation results show that, while moving along the slit, the mononucleotides are adsorbed and desorbed from the walls multiple times. For the simulations, the estimated minimum slit length required for separation of the dNMP flight time distributions is about 5.9 μm, and the minimum analysis time per dNMP is about 10 μs. These are determined by the nature of the nucleotide-wall interactions, channel width, and by the flow characteristics. A simple analysis using realistic dNMP velocities shows that, in order to reduce the effects of diffusional broadening and keep the analysis time per dNMP reasonably small, the nucleotide velocity should be relatively high. Tailored surface chemistry could lead to further reduction of the analysis time toward its minimum value for a given driving force.
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Affiliation(s)
- Brian R Novak
- Department of Mechanical and Industrial Engineering, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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28
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Wang H, Silva A, Ho CM. When Medicine Meets Engineering-Paradigm Shifts in Diagnostics and Therapeutics. Diagnostics (Basel) 2013; 3:126-54. [PMID: 26835672 PMCID: PMC4665584 DOI: 10.3390/diagnostics3010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/10/2013] [Accepted: 01/23/2013] [Indexed: 01/09/2023] Open
Abstract
During the last two decades, the manufacturing techniques of microfluidics-based devices have been phenomenally advanced, offering unlimited potential for bio-medical technologies. However, the direct applications of these technologies toward diagnostics and therapeutics are still far from maturity. The present challenges lay at the interfaces between the engineering systems and the biocomplex systems. A precisely designed engineering system with narrow dynamic range is hard to seamlessly integrate with the adaptive biological system in order to achieve the design goals. These differences remain as the roadblock between two fundamentally non-compatible systems. This paper will not extensively review the existing microfluidic sensors and actuators; rather, we will discuss the sources of the gaps for integration. We will also introduce system interface technologies for bridging the differences to lead toward paradigm shifts in diagnostics and therapeutics.
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Affiliation(s)
- Hann Wang
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aleidy Silva
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chih-Ming Ho
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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29
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Insertion kinetics of small nucleotides through single walled carbon nanotube. J Biotechnol 2012; 164:13-8. [PMID: 23262130 DOI: 10.1016/j.jbiotec.2012.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 11/22/2022]
Abstract
We report molecular dynamic simulations showing that a DNA molecule constituted by five unique bases can be spontaneously inserted into single walled carbon nanotube (SWCNT) in normal conditions (P, T and water environment) depending on the tube radius value. The van der Waals and electrostatic interactions play a central role for the rapid insertion process. Our study shows also that the Guanine molecule inserts the fastest compared to thymine, adenine and cytosine bases, respectively. The differences of insertion time could be exploited for applications concerning for example DNA sequencing.
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30
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Campos E, Asandei A, McVey CE, Dias JC, Oliveira ASF, Soares CM, Luchian T, Astier Y. The role of Lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15643-15650. [PMID: 23046444 DOI: 10.1021/la302613g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single channel recordings were used to determine the effect of direct electrostatic interactions between sulfonate-coated gold nanoparticles and the constriction of the Staphylococcus aureus α-hemolysin protein channel on the ionic current amplitude. We provide evidence that Lys147 of α-hemolysin can interact with the sulfonate groups at the nanoparticle surface, and these interactions can reversibly block 100% of the residual ionic current. Lys147 is normally involved in a salt bridge with Glu111. The capture of a nanoparticle leads to a partial current block at neutral pH values, but protonation of Glu111 at pH 2.8 results in a full current block when the nanoparticle is captured. At pH 2.8, we suggest that Lys147 is free to engage in electrostatic interactions with sulfonates at the nanoparticle surface. To verify our results, we engineered a mutation in the α-hemolysin protein, where Glu111 is substituted by Ala (E111A), thus removing Glu111-Lys147 interactions and facilitating Lys147-sulfonate electrostatic interactions. This mutation leads to a 100% current block at pH 2.8 and a 92% block at pH 8.0, showing that electrostatic interactions are formed between the nanopore and the nanoparticle surface. Besides demonstrating the effect of electrostatic interactions on cross channel ionic current, this work offers a novel approach to controlling open and closed states of the α-hemolysin nanopore as a function of external gears.
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Affiliation(s)
- Elisa Campos
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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31
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Abstract
Molecular dynamics simulation is utilized to investigate the ionic transport of NaCl in solution through a graphene nanopore under an applied electric field. Results show the formation of concentration polarization layers in the vicinity of the graphene sheet. The nonuniformity of the ion distribution gives rise to an electric pressure which drives vortical motions in the fluid if the electric field is sufficiently strong to overcome the influence of viscosity and thermal fluctuations. The relative importance of hydrodynamic transport and thermal fluctuations in determining the pore conductivity is investigated. A second important effect that is observed is the mass transport of water through the nanopore, with an average velocity proportional to the applied voltage and independent of the pore diameter. The flux arises as a consequence of the asymmetry in the ion distribution which can be attributed to differing mobilities of the sodium and chlorine ions and to the polarity of water molecules. The accumulation of liquid molecules in the vicinity of the nanopore due to re-orientation of the water dipoles by the local electric field is seen to result in a local increase in the liquid density. Results confirm that the electric conductance is proportional to the nanopore diameter for the parameter regimes that we simulated. The occurrence of fluid vortices is found to result in an increase in the effective electrical conductance.
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Affiliation(s)
- Guohui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Modern Mechanics Division, E-Institutes of Shanghai Universities, Shanghai University, 149 Yanchang Road, Shanghai 200072, People's Republic of China
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32
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Abstract
We describe here a method for detecting the translocation of individual DNA molecules through nanopores created in graphene membranes. The devices consist of 1-5-nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, and the reduced electrical resistance, we observe larger blocked currents than for traditional solid-state nanopores. We also show how ionic current noise levels can be reduced with the atomic-layer deposition of a few nanometers of titanium dioxide over the graphene surface. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor, and its use opens the door to a new future class of nanopore devices in which electronic sensing and control is performed directly at the pore.
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Affiliation(s)
- Chris A Merchant
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
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33
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He Y, Tsutsui M, Taniguchi M, Kawai T. DNA capture in nanopores for genome sequencing: challenges and opportunities. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31495a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Purnell R, Schmidt J. Measurements of DNA immobilized in the alpha-hemolysin nanopore. Methods Mol Biol 2012; 870:39-53. [PMID: 22528257 DOI: 10.1007/978-1-61779-773-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In the past decade, there have been extensive studies aimed at exploring the potential of protein nanopores to sequence single strands of DNA using resistive pulse sensing. The high speed of DNA electrophoretically driven through these pores (∼l μs/base) necessitates high bandwidth measurements, which prevent resolution of the picoampere differences in blockage current resulting from different nucleotides. Here, we describe a procedure for the immobilization of DNA in the α-hemolysin protein nanopore which enables low-noise, high-precision measurements capable of resolving subpicoampere differences in blockage current associated with differences in the sequence and structure of the DNA.
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Affiliation(s)
- Robert Purnell
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, CA, USA
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35
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Abstract
Nanopore analysis is an emerging technique that involves using a voltage to drive molecules through a nanoscale pore in a membrane between two electrolytes, and monitoring how the ionic current through the nanopore changes as single molecules pass through it. This approach allows charged polymers (including single-stranded DNA, double-stranded DNA and RNA) to be analysed with subnanometre resolution and without the need for labels or amplification. Recent advances suggest that nanopore-based sensors could be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000. In this article we review the use of nanopore technology in DNA sequencing, genetics and medical diagnostics.
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Affiliation(s)
- Bala Murali Venkatesan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
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36
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Liebes Y, Hadad B, Ashkenasy N. Effects of electrons on the shape of nanopores prepared by focused electron beam induced etching. NANOTECHNOLOGY 2011; 22:285303. [PMID: 21636881 DOI: 10.1088/0957-4484/22/28/285303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The fabrication of nanometric pores with controlled size is important for applications such as single molecule detection. We have recently suggested the use of focused electron beam induced etching (FEBIE) for the preparation of such nanopores in silicon nitride membranes. The use of a scanning probe microscope as the electron beam source makes this technique comparably accessible, opening the way to widespread fabrication of nanopores. Since the shape of the nanopores is critically important for their performance, in this work we focus on its analysis and study the dependence of the nanopore shape on the electron beam acceleration voltage. We show that the nanopore adopts a funnel-like shape, with a central pore penetrating the entire membrane, surrounded by an extended shallow-etched region at the top of the membrane. While the internal nanopore size was found to depend on the electron acceleration voltage, the nanopore edges extended beyond the primary electron beam spot size due to long-range effects, such as radiolysis and diffusion. Moreover, the size of the peripheral-etched region was found to be less dependent on the acceleration voltage. We also found that chemical etching is the rate-limiting step of the process and is only slightly dependent on the acceleration voltage. Furthermore, due to the chemical etch process the chemical composition of the nanopore rims was found to maintain the bulk membrane composition.
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Affiliation(s)
- Yael Liebes
- Department of Materials Engineering, Ben-Gurion University of the Negev, PO Box 653 Beer-Sheva, Israel
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37
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Zhang M, Ai Y, Sharma A, Joo SW, Kim DS, Qian S. Electrokinetic particle translocation through a nanopore containing a floating electrode. Electrophoresis 2011; 32:1864-74. [DOI: 10.1002/elps.201100050] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 02/28/2011] [Accepted: 03/10/2011] [Indexed: 11/10/2022]
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38
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Lolicato M, Reina S, Messina A, Guarino F, Winterhalter M, Benz R, De Pinto V. Generation of artificial channels by multimerization of β-strands from natural porin. Biol Chem 2011; 392:617-24. [PMID: 21627534 DOI: 10.1515/bc.2011.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
General diffusion porins are passive transmembrane channels. We have explored the possibility to create artificial nanopores starting from natural β-barrel structures. Structural elements of bacterial porins were used to build a series of artificial nanopores. The basic module was selected by multi-alignment of general diffusion porins. The sequence corresponded to a highly conserved motif containing two β-strands, which was obtained from Escherichia coli OmpF. Dimeric to octameric repeats were obtained through cDNA recombinant technology. The hexameric repeat was used to test its properties. This protein was expressed, purified and reconstituted in the planar bilayer membranes. It was able to form channels in membranes with a conductance of 300 pS in 150 mm KCl and did not show any relevant voltage-dependence.
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Affiliation(s)
- Marco Lolicato
- Department of Biology, Laboratory of Biochemistry and Molecular Biology, University of Catania, Italy
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39
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Guo F, Mukhopadhyay A, Sheldon BW, Hurt RH. Vertically aligned graphene layer arrays from chromonic liquid crystal precursors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:508-513. [PMID: 21254253 DOI: 10.1002/adma.201003158] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 10/12/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Fei Guo
- Institute for Molecular and Nanoscale Innovation, Brown University, Providence, Rhode Island 02912, USA
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40
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Abstract
Nanoparticle electrophoretic translocation through a single nanopore induces a detectable change in the ionic current, which enables the nanopore-based sensing for various bio-analytical applications. In this study, a transient continuum-based model is developed for the first time to investigate the electrokinetic particle translocation through a nanopore by solving the Nernst-Planck equations for the ionic concentrations, the Poisson equation for the electric potential and the Navier-Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian (ALE) method. When the applied electric field is relatively low, a current blockade is expected. In addition, the particle could be trapped at the entrance of the nanopore when the electrical double layer (EDL) adjacent to the charged particle is relatively thick. When the electric field imposed is relatively high, the particle can always pass through the nanopore by electrophoresis. However, a current enhancement is predicted if the EDL of the particle is relatively thick. The obtained numerical results qualitatively agree with the existing experimental results. It is also found that the initial orientation of the particle could significantly affect the particle translocation and the ionic current through a nanopore. Furthermore, a relatively high electric field tends to align the particle with its longest axis parallel to the local electric field. However, the particle's initial lateral offset from the centerline of the nanopore acts as a minor effect.
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Affiliation(s)
- Ye Ai
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
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41
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Abstract
The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management.
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Affiliation(s)
- Fabricio F Costa
- Cancer Biology and Epigenomics Program, Children's Memorial Research Center and Northwestern University's Feinberg School of Medicine, 2430 N. Halsted St, Box 220, Chicago, IL, USA
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42
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Ai Y, Liu J, Zhang B, Qian S. Field Effect Regulation of DNA Translocation through a Nanopore. Anal Chem 2010; 82:8217-25. [DOI: 10.1021/ac101628e] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ye Ai
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan 430074, China, and School of Mechanical Engineering, Yeungnam University, Gyongsan 712-749, South Korea
| | - Jing Liu
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan 430074, China, and School of Mechanical Engineering, Yeungnam University, Gyongsan 712-749, South Korea
| | - Bingkai Zhang
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan 430074, China, and School of Mechanical Engineering, Yeungnam University, Gyongsan 712-749, South Korea
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, Wuhan 430074, China, and School of Mechanical Engineering, Yeungnam University, Gyongsan 712-749, South Korea
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43
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Merchant CA, Healy K, Wanunu M, Ray V, Peterman N, Bartel J, Fischbein MD, Venta K, Luo Z, Johnson ATC, Drndić M. DNA translocation through graphene nanopores. NANO LETTERS 2010; 10:2915-21. [PMID: 20698604 DOI: 10.1021/nl101046t] [Citation(s) in RCA: 557] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.
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Affiliation(s)
- Christopher A Merchant
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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44
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van den Hout M, Hall AR, Wu MY, Zandbergen HW, Dekker C, Dekker NH. Controlling nanopore size, shape and stability. NANOTECHNOLOGY 2010; 21:115304. [PMID: 20173233 DOI: 10.1088/0957-4484/21/11/115304] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Solid-state nanopores are considered a promising tool for the study of biological polymers such as DNA and RNA, due largely to their flexibility in size, potential in device integration and robustness. Here, we show that the precise shape of small nanopores (approximately 5 nm diameter in 20 nm SiN membranes) can be controlled by using transmission electron microscope (TEM) beams of different sizes. However, when some of these small nanopores are immersed in an aqueous solution, their resistance is observed to decrease over time. By comparing nanopores of different shapes using (scanning) TEM both before and after immersion in aqueous solution, we demonstrate that the stability of small nanopores is related to their three-dimensional geometry, which depends on the TEM beam size employed during pore fabrication. Optimal stability is obtained using a TEM beam size of approximately the same size as the intended nanopore diameter. In addition, we show that thermal oxidation can serve as a means to independently control nanopore size following TEM fabrication. These observations provide key guidelines for the fabrication of stable solid-state nanopores on the scale of nucleic acids and small proteins.
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Affiliation(s)
- Michiel van den Hout
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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45
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Joseph S, Guan W, Reed MA, Krstic PS. A long DNA segment in a linear nanoscale Paul trap. NANOTECHNOLOGY 2010; 21:015103. [PMID: 19946172 PMCID: PMC3269948 DOI: 10.1088/0957-4484/21/1/015103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We study the dynamics of a linearly distributed line charge such as single stranded DNA (ssDNA) in a nanoscale, linear 2D Paul trap in vacuum. Using molecular dynamics simulations we show that a line charge can be trapped effectively in the trap for a well defined range of stability parameters. We investigated (i) a flexible bonded string of charged beads and (ii) a ssDNA polymer of variable length, for various trap parameters. A line charge undergoes oscillations or rotations as it moves, depending on its initial angle, the position of the center of mass and the velocity. The stability region for a strongly bonded line of charged beads is similar to that of a single ion with the same charge to mass ratio. Single stranded DNA as long as 40 nm does not fold or curl in the Paul trap, but could undergo rotations about the center of mass. However, we show that a stretching field in the axial direction can effectively prevent the rotations and increase the confinement stability.
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Affiliation(s)
- Sony Joseph
- Physics Division, Oak Ridge National Laboratory, P. O. Box 2008, Oak Ridge, TN 37831, USA
| | - Weihua Guan
- Department of Electrical Engineering, Yale University, New Haven, CT 06520, USA
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Applied Physics, Yale University, New Haven, CT 06520, USA
| | - Predrag S. Krstic
- Physics Division, Oak Ridge National Laboratory, P. O. Box 2008, Oak Ridge, TN 37831, USA
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46
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Piruska A, Gong M, Sweedler JV, Bohn PW. Nanofluidics in chemical analysis. Chem Soc Rev 2010; 39:1060-72. [DOI: 10.1039/b900409m] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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47
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Murday JS, Siegel RW, Stein J, Wright JF. Translational nanomedicine: status assessment and opportunities. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2009; 5:251-73. [PMID: 19540359 DOI: 10.1016/j.nano.2009.06.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/07/2009] [Indexed: 10/20/2022]
Abstract
UNLABELLED Nano-enabled technologies hold great promise for medicine and health. The rapid progress by the physical sciences/engineering communities in synthesizing nanostructures and characterizing their properties must be rapidly exploited in medicine and health toward reducing mortality rate, morbidity an illness imposes on a patient, disease prevalence, and general societal burden. A National Science Foundation-funded workshop, "Re-Engineering Basic and Clinical Research to Catalyze Translational Nanoscience," was held 16-19 March 2008 at the University of Southern California. Based on that workshop and literature review, this article briefly explores scientific, economic, and societal drivers for nanomedicine initiatives; examines the science, engineering, and medical research needs; succinctly reviews the US federal investment directly germane to medicine and health, with brief mention of the European Union (EU) effort; and presents recommendations to accelerate the translation of nano-enabled technologies from laboratory discovery into clinical practice. FROM THE CLINICAL EDITOR An excellent review paper based on the NSF funded workshop "Re-Engineering Basic and Clinical Research to Catalyze Translational Nanoscience" (16-19 March 2008) and extensive literature search, this paper briefly explores the current state and future perspectives of nanomedicine.
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Affiliation(s)
- James S Murday
- University of Southern California, Washington, DC 20004 USA.
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48
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Lemay SG. Nanopore-based biosensors: the interface between ionics and electronics. ACS NANO 2009; 3:775-779. [PMID: 19397344 DOI: 10.1021/nn900336j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Techniques for translating the binding or the activity of single molecules directly into electrical signals are of interest for both fundamental and applied science. A paper in this issue describes experiments in which the ionic current through a biological nanopore is employed both to control and to monitor the attachment of individual DNA polymerase enzymes to their binding site on a single DNA molecule. This Perspective briefly sketches some of the factors that ultimately limit the performance of such nanoscale sensors, emphasizing in particular the interface between nanofluidic systems and external control electronics.
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Affiliation(s)
- Serge G Lemay
- Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
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49
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Abstract
Low-frequency ionic current noise in solid-state nanopores imposes a limitation on the time resolution achieved in translocation experiments. Recently, this 1/f noise was described as obeying Hooge's phenomenological relation, where the noise scales inversely with the number of charge carriers present. Here, we consider an alternative model in which the low-frequency noise originates from surface charge fluctuations. We compare the models and show that Hooge's relation gives the best description for the low-frequency noise in solid-state nanopores over the entire salt regime from 10(-3) to 1.6 M KCl.
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Affiliation(s)
- R M M Smeets
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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50
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Voelkerding KV, Dames SA, Durtschi JD. Next-generation sequencing: from basic research to diagnostics. Clin Chem 2009; 55:641-58. [PMID: 19246620 DOI: 10.1373/clinchem.2008.112789] [Citation(s) in RCA: 433] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). CONTENT This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. SUMMARY In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.
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Affiliation(s)
- Karl V Voelkerding
- ARUP Institute for Experimental and Clinical Pathology, Salt Lake City, Utah 84108, USA.
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