1
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Caglayan MO, Şahin S, Üstündağ Z. Detection Strategies of Zearalenone for Food Safety: A Review. Crit Rev Anal Chem 2020; 52:294-313. [PMID: 32715728 DOI: 10.1080/10408347.2020.1797468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Zearalenone (ZEN) is a toxic compound produced by the metabolism of fungi (genus Fusarium) that threaten the food and agricultural industry belonging to the in foods and feeds. ZEN has toxic effects on human and animal health due to its mutagenicity, teratogenicity, carcinogenicity, nephrotoxicity, immunotoxicity, and genotoxicity. To ensure food safety, rapid, precise, and reliable analytical methods can be developed for the detection of toxins such as ZEN. Different selective molecular diagnostic elements are used in conjunction with different detection strategies to achieve this goal. In this review, the use of electrochemical, colorimetric, fluorometric, refractometric as well as other strategies were discussed for ZEN detection. The success of the sensors in analytical performance depends on the development of receptors with increased affinity to the target. This requirement has been met with different immunoassays, aptamer-assays, and molecular imprinting techniques. The immobilization techniques and analysis strategies developed with the combination of nanomaterials provided high precision, reliability, and convenience in ZEN detection, in which electrochemical strategies perform the best.
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Affiliation(s)
| | - Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, Kütahya, Turkey
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2
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Diagnostic and Therapeutic Value of Aptamers in Envenomation Cases. Int J Mol Sci 2020; 21:ijms21103565. [PMID: 32443562 PMCID: PMC7278915 DOI: 10.3390/ijms21103565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
It is now more than a century since Albert Calmette from the Institut Pasteur changed the world of envenomation by demonstrating that antibodies raised against animal venoms have the ability to treat human victims of previously fatal bites or stings. Moreover, the research initiated at that time effectively launched the discipline of toxicology, first leading to the search for toxic venom components, followed by the demonstration of venoms that also contained compounds of therapeutic value. Interest from pharmaceutical companies to treat envenomation is, however, declining, mainly for economic reasons, and hence, the World Health Organization has reclassified this public health issue to be a highest priority concern. While the production, storage, and safety of antivenom sera suffer from major inconveniences, alternative chemical and technological approaches to the problem of envenomation need to be considered that bypass the use of antibodies for toxin neutralization. Herein, we review an emerging strategy that relies on the use of aptamers and discuss how close—or otherwise—we are to finding a viable alternative to the use of antibodies for the therapy of human envenomation.
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3
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Fraser LA, Cheung YW, Kinghorn AB, Guo W, Shiu SCC, Jinata C, Liu M, Bhuyan S, Nan L, Shum HC, Tanner JA. Microfluidic Technology for Nucleic Acid Aptamer Evolution and Application. ACTA ACUST UNITED AC 2019; 3:e1900012. [PMID: 32627415 DOI: 10.1002/adbi.201900012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/12/2019] [Indexed: 12/18/2022]
Abstract
The intersection of microfluidics and aptamer technologies holds particular promise for rapid progress in a plethora of applications across biomedical science and other areas. Here, the influence of microfluidics on the field of aptamers, from traditional capillary electrophoresis approaches through innovative modern-day approaches using micromagnetic beads and emulsion droplets, is reviewed. Miniaturizing aptamer-based bioassays through microfluidics has the potential to transform diagnostics and embedded biosensing in the coming years.
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Affiliation(s)
- Lewis A Fraser
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Soubhagya Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Lang Nan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
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4
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Bruno JG. Potential Inherent Stimulation of the Innate Immune System by Nucleic Acid Aptamers and Possible Corrective Approaches. Pharmaceuticals (Basel) 2018; 11:ph11030062. [PMID: 29937498 PMCID: PMC6161019 DOI: 10.3390/ph11030062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/25/2023] Open
Abstract
It is well known that unmethylated 2′-deoxycytidine-phosphate-2′-guanine (CpG) sequences alone or in longer DNA and RNA oligonucleotides can act like pathogen-associated molecular patterns (PAMPs) and trigger the innate immune response leading to deleterious cytokine production via Toll-like receptors (TLRs). Clearly, such CpG or CpG-containing sequences in aptamers intended for therapy could present very damaging side effects to patients. Previous antisense oligonucleotide developers were faced with the same basic CpG dilemma and devised not only avoidance, but other effective strategies from which current aptamer developers can learn to ameliorate or eliminate damaging CpG effects. These strategies include obvious methylation of cytosines in the aptamer structure, as long as it does not affect aptamer binding in vivo, truncation of the aptamer to its essential binding site, backbone modifications, co-administration of antagonistic or suppressive oligonucleotides, or other novel drugs under development to lessen the toxic CpG effect on innate immunity.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, TX 78229, USA.
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5
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Cao C, Zhang F, Goldys EM, Gao F, Liu G. Advances in structure-switching aptasensing towards real time detection of cytokines. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Luo CH, Yeh CS. Construction of Deoxyribonucleic Acid Decorated Gold Nanostructures as Nanomedical Agents. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201700255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cheng-Hung Luo
- Department of Chemistry; National Cheng Kung University; Tainan 701 Taiwan
| | - Chen-Sheng Yeh
- Department of Chemistry; National Cheng Kung University; Tainan 701 Taiwan
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7
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Li CH, Xiao X, Tao J, Wang DM, Huang CZ, Zhen SJ. A graphene oxide-based strand displacement amplification platform for ricin detection using aptamer as recognition element. Biosens Bioelectron 2017; 91:149-154. [PMID: 28006682 DOI: 10.1016/j.bios.2016.12.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
The toxic plant protein ricin is a potential agent for criminal or bioterrorist attacks due to the wide availability and relative ease of preparation. Herein, we developed a novel strategy for the detection of ricin B-chain (RTB) based on isothermal strand-displacement polymerase reaction (ISDPR) by using aptamer as a recognition element and graphene oxide (GO) as a low background platform. In this method, ricin-binding aptamer (RBA) hybridized with a short blocker firstly, and then was immobilized on the surface of streptavidin-coated magnetic beads (MBs). The addition of RTB could release the blocker, which could hybridize with the dye-modified hairpin probe and trigger the ISDPR, resulting in high fluorescence intensity. In the absence of RTB, however, the fluorescence of the dye could be quenched strongly by GO, resulting in the extremely low background signal. Thus, RTB could be sensitively detected by the significantly increased fluorescence signal. The linear range of the current analytical system was from 0.75μg/mL to 100μg/mL and the limit of detection (3σ) was 0.6μg/mL. This method has been successfully utilized for the detection of both the RTB and the entire ricin toxin in real samples, and it could be generalized to any kind of target detection based on an appropriate aptamer.
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Affiliation(s)
- Chun Hong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China
| | - Xue Xiao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China
| | - Jing Tao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China
| | - Dong Mei Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China; College of Pharmaceutical Sciences, Southwest University, 400715 Chongqing, PR China.
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715 Chongqing, PR China.
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8
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Ren S, Shin HS, Gedi V, Dua P, Lee DK, Kim S. Selection of DNA Aptamers Against Botulinum Neurotoxin E for Development of Fluorescent Aptasensor. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shuo Ren
- Department of Biomedical Engineering; Dongguk University; Seoul 100-715 Korea
| | - Hye-Soo Shin
- Global Research Laboratory (GRL) for RNAi Medicine, Department of Chemistry; Sungkyunkwan University; Suwon 16419 Korea
| | - Vinayakumar Gedi
- Global Research Laboratory (GRL) for RNAi Medicine, Department of Chemistry; Sungkyunkwan University; Suwon 16419 Korea
| | - Pooja Dua
- Global Research Laboratory (GRL) for RNAi Medicine, Department of Chemistry; Sungkyunkwan University; Suwon 16419 Korea
| | - Dong-Ki Lee
- Global Research Laboratory (GRL) for RNAi Medicine, Department of Chemistry; Sungkyunkwan University; Suwon 16419 Korea
| | - Soyoun Kim
- Department of Biomedical Engineering; Dongguk University; Seoul 100-715 Korea
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9
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Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
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Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
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10
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Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection. Biosens Bioelectron 2016; 85:822-827. [PMID: 27295569 DOI: 10.1016/j.bios.2016.05.091] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 05/30/2016] [Indexed: 11/23/2022]
Abstract
Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer.
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11
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Ye F, Mi Q, Zhang N, Li X, Yu J, Gao Z, Zheng Y, Fan Q, Wang J, Wang J. Probing the Key Binding Sequence and Improvement of the Stability of a β-Bungarotoxin-binding Aptamer in Snake Venom. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fengping Ye
- State Key Laboratory of Pathogen and Biosecurity; Institute of Microbiology and Epidemiology; Beijing 100071 China
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
| | - Qili Mi
- Technology Center; China Tobacco Yunnan Industrial Co., Ltd; Kunming 650231 China
| | - Ning Zhang
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
- Hospital of Unit 77256, PLA; Kunming 650225 China
| | - Xuemei Li
- Technology Center; China Tobacco Yunnan Industrial Co., Ltd; Kunming 650231 China
| | - Jing Yu
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
| | - Zhongping Gao
- Medical Department; General Hospital of Qinghai Armed Police; Xining 810000 China
| | - Ying Zheng
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
| | - Quanshui Fan
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
| | - Jie Wang
- Institute of Military Medicine; Chengdu Military Region's Center for Disease Control & Prevention; Kunming 650032 China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity; Institute of Microbiology and Epidemiology; Beijing 100071 China
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12
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Wang CC, Wu SM, Li HW, Chang HT. Biomedical Applications of DNA-Conjugated Gold Nanoparticles. Chembiochem 2016; 17:1052-62. [PMID: 26864481 DOI: 10.1002/cbic.201600014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 01/07/2023]
Abstract
Gold nanoparticles (AuNPs) are useful for diagnostic and biomedical applications, mainly because of their ease in preparation and conjugation, biocompatibility, and size-dependent optical properties. However, bare AuNPs do not possess specificity for targets. AuNPs conjugated with DNA aptamers offer specificity for various analytes, such as proteins and small molecules/ions. Although DNA aptamers themselves have therapeutic and target-recognizing properties, they are susceptible to degradation in vivo. When DNA aptamers are conjugated to AuNPs, their stability and cell uptake efficiency both increase, making aptamer-AuNPs suitable for biomedical applications. Additionally, drugs can be efficiently conjugated with DNA aptamer-AuNPs to further enhance their therapeutic efficiency. This review focuses on the applications of DNA aptamer-based AuNPs in several biomedical areas, including anticoagulation, anticancer, antibacterial, and antiviral applications.
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Affiliation(s)
- Chun-Chi Wang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Shou-Mei Wu
- School of Pharmacy, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung, 80708, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
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13
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Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. Molecules 2015; 20:20832-40. [PMID: 26610452 PMCID: PMC6332122 DOI: 10.3390/molecules201119733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming RNAs located within the pre-mRNA. We showed that the G4 in the 5′ UTR and first intron of VEGFA bound to the protein encoded in VEGFA gene, VEGF165, with high affinity. Moreover, G4-forming RNAs located within the PDGFA and the PDGFB introns bound to PDGF-AA and PDGF-BB, respectively, indicating that G4 in the pre-mRNA could be an aptamer. It had been reported that the putative G4-forming RNA sequences are located in some parts of most genes, thus our strategy for aptamer identification could be applicable to other proteins. It has been reported that some G4-forming RNAs in 5′ UTRs are involved in translation control; however, G4-forming excised intronic RNA function has not been revealed previously. Therefore, these findings could not only contribute to the identification of RNA aptamers but also provide new insights into the biological functioning of G4-forming RNAs located within intronic RNA sequences.
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14
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Advances in Anthrax Detection: Overview of Bioprobes and Biosensors. Appl Biochem Biotechnol 2015; 176:957-77. [PMID: 25987133 DOI: 10.1007/s12010-015-1625-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 04/08/2015] [Indexed: 12/22/2022]
Abstract
Anthrax is an infectious disease caused by Bacillus anthracis. Although anthrax commonly affects domestic and wild animals, it causes a rare but lethal infection in humans. A variety of techniques have been introduced and evaluated to detect anthrax using cultures, polymerase chain reaction, and immunoassays to address the potential threat of anthrax being used as a bioweapon. The high-potential harm of anthrax in bioterrorism requires sensitive and specific detection systems that are rapid, field-ready, and real-time monitoring. Here, we provide a systematic overview of anthrax detection probes with their potential applications in various ultra-sensitive diagnostic systems.
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15
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Ye F, Zheng Y, Wang X, Tan X, Zhang T, Xin W, Wang J, Huang Y, Fan Q, Wang J. Recognition of Bungarus multicinctus venom by a DNA aptamer against β-bungarotoxin. PLoS One 2014; 9:e105404. [PMID: 25144237 PMCID: PMC4140777 DOI: 10.1371/journal.pone.0105404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/21/2014] [Indexed: 01/03/2023] Open
Abstract
Antibody-based technology is the main method for diagnosis and treatment of snake bite envenoming currently. However, the development of an antibody, polyclonal or monoclonal, is a complicated and costly procedure. Aptamers are single stranded oligonucleotides that recognize specific targets such as proteins and have shown great potential over the years as diagnostic and therapeutic agents. In contrast to antibodies, aptamers can be selected in vitro without immunization of animals, and synthesized chemically with extreme accuracy, low cost and high degree of purity. In this study we firstly report on the identification of DNA aptamers that bind to β-bungarotoxin (β-BuTx), a neurotoxin from the venom of Bungarus multicinctus. A plate-SELEX method was used for the selection of β-BuTx specific aptamers. After 10 rounds of selection, four aptamer candidates were obtained, with the dissociation constant ranged from 65.9 nM to 995 nM measured by fluorescence spectroscopy. Competitive binding assays using both the fluorescently labeled and unlabeled aptamers revealed that the four aptamers bound to the same binding site of β-BuTx. The best binder, βB-1, bound specifically to β-BuTx, but not to BSA, casein or α-Bungarotoxin. Moreover, electrophoretic mobility shift assay and enzyme-linked aptamer assay demonstrated that βB-1 could discriminate B. multicinctus venom from other snake venoms tested. The results suggest that aptamer βB-1 can serve as a useful tool for the design and development of drugs and diagnostic tests for β-BuTx poisoning and B. multicinctus bites.
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Affiliation(s)
- Fengping Ye
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Ying Zheng
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xi Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xiaolong Tan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Tao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Jie Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Yong Huang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Quanshui Fan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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16
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Nucleic acid aptamers: research tools in disease diagnostics and therapeutics. BIOMED RESEARCH INTERNATIONAL 2014; 2014:540451. [PMID: 25050359 PMCID: PMC4090538 DOI: 10.1155/2014/540451] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
Abstract
Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.
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17
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Szeitner Z, András J, Gyurcsányi RE, Mészáros T. Is less more? Lessons from aptamer selection strategies. J Pharm Biomed Anal 2014; 101:58-65. [PMID: 24877649 DOI: 10.1016/j.jpba.2014.04.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 12/19/2022]
Abstract
Aptamers have many inherent advantages originating from their in vitro selection and tailored chemical synthesis that makes them appealing alternatives of antibodies in bioaffinity assays. However, what ultimately matters, and that is the prerequisite to give way to all these advantages, is how well, and how selectively the aptamers bind to their targets. With the aptamer selection largely in the hand of life scientists, analytical chemists focused mostly on methodological development of aptamer-based assays using a fairly restricted number of aptamers to prove their concepts. However, ideally the development of an aptamer-based assay should start from the selection of aptamers to ensure their proper functionality in real samples. For instance information on the sample matrix can be implemented within counter-selection steps to discard aptamer candidates that show cross-reactivity to matrix components or critical interferents. In general, a larger consideration of the analytical use during selection and characterization of aptamers have been shown to increase the applicability of aptamers. Therefore, this review is a short, subjective view on trends in aptamer development highlighting factors to consider during their selection for a successful analytical application.
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Affiliation(s)
- Zsuzsanna Szeitner
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| | - Judit András
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary; MTA-BME Technical Analytical Chemistry Research Group of the Hungarian Academy of Sciences, Szent Gellért tér 4, H-1111 Budapest, Hungary.
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18
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Challa S, Tzipori S, Sheoran A. Selective Evolution of Ligands by Exponential Enrichment to Identify RNA Aptamers against Shiga Toxins. J Nucleic Acids 2014; 2014:214929. [PMID: 24839553 PMCID: PMC4009280 DOI: 10.1155/2014/214929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/06/2014] [Accepted: 03/25/2014] [Indexed: 12/21/2022] Open
Abstract
Infection with Shiga toxin- (Stx-) producing E. coli causes life threatening hemolytic uremic syndrome (HUS), a leading cause of acute renal failure in children. Of the two antigenically distinct toxins, Stx1 and Stx2, Stx2 is more firmly linked with the development of HUS. In the present study, selective evolution of ligands by exponential enrichment (SELEX) was used in an attempt to identify RNA aptamers against Stx1 and Stx2. After 5 rounds of selection, significant enrichment of aptamer pool was obtained against Stx2, but not against Stx1, using a RNA aptamer library containing 56 random nucleotides (N56). Characterization of individual aptamer sequences revealed that six unique RNA aptamers (mA/pC, mB/pA, mC, mD, pB, and pD) recognized Stx2 in a filter binding assay. None of these aptamers bound Stx1. Aptamers mA/pC, mB/pA, mC, and mD, but not pB and pD, partially blocked binding of Alexa 488-labeled Stx2 with HeLa cells in a flow cytometry assay. However, none of the aptamers neutralized Stx2-mediated cytotoxicity and death of HeLa cells.
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Affiliation(s)
- Sreerupa Challa
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, Building 20, North Grafton, MA 01536, USA
- AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, Building 20, North Grafton, MA 01536, USA
| | - Abhineet Sheoran
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, Building 20, North Grafton, MA 01536, USA
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Sapag A, Salinas-Luypaert C, Constenla-Muñoz C. First report of in vitro selection of RNA aptamers targeted to recombinant Loxosceles laeta spider toxins. Biol Res 2014; 47:2. [PMID: 25027855 PMCID: PMC4060373 DOI: 10.1186/0717-6287-47-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Loxoscelism is the envenomation caused by the bite of Loxosceles spp. spiders. It entails severe necrotizing skin lesions, sometimes accompanied by systemic reactions and even death. There are no diagnostic means and treatment is mostly palliative. The main toxin, found in several isoforms in the venom, is sphingomyelinase D (SMD), a phospholipase that has been used to generate antibodies intended for medical applications. Nucleic acid aptamers are a promising alternative to antibodies. Aptamers may be isolated from a combinatorial mixture of oligonucleotides by iterative selection of those that bind to the target. In this work, two Loxosceles laeta SMD isoforms, Ll1 and Ll2, were produced in bacteria and used as targets with the aim of identifying RNA aptamers that inhibit sphingomyelinase activity. RESULTS Six RNA aptamers capable of eliciting partial but statistically significant inhibitions of the sphingomyelinase activity of recombinant SMD-Ll1 and SMD-Ll2 were obtained: four aptamers exert ~17% inhibition of SMD-Ll1, while two aptamers result in ~25% inhibition of SMD-Ll2 and ~18% cross inhibition of SMD-Ll1. CONCLUSIONS This work is the first attempt to obtain aptamers with therapeutic and diagnostic potential for loxoscelism and provides an initial platform to undertake the development of novel anti Loxosceles venom agents.
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Yoshida W, Abe K, Ikebukuro K. Emerging techniques employed in aptamer-based diagnostic tests. Expert Rev Mol Diagn 2014; 14:143-51. [PMID: 24400930 DOI: 10.1586/14737159.2014.868307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since aptamers were reported in 1990, research into the applications of aptamers, particularly diagnostic applications, has been growing. Aptamers can act as recognition elements instead of antibodies. In this regard, aptamers have unique characteristics because they are composed of nucleic acids. Intra- and intermolecular interactions of nucleic acids can be easily tailored following straightforward hybridization rules. Nucleic acids can be enzymatically replicated and their sequences can be determined using high-throughput methods. Using these properties, ligand-induced structural change-based aptamer sensors for homogeneous assays, polymerase- and/or nuclease-combined aptamer sensors for ultrasensitive assays, and microarray/next-generation sequencing-based aptamer sensors for multiplexed assays have been developed. This article reviews these unique aptamer sensors, demonstrating their great potential for diagnostic applications.
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Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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21
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Amaya-González S, de-los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Aptamer-based analysis: a promising alternative for food safety control. SENSORS (BASEL, SWITZERLAND) 2013; 13:16292-311. [PMID: 24287543 PMCID: PMC3892839 DOI: 10.3390/s131216292] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023]
Abstract
Ensuring food safety is nowadays a top priority of authorities and professional players in the food supply chain. One of the key challenges to determine the safety of food and guarantee a high level of consumer protection is the availability of fast, sensitive and reliable analytical methods to identify specific hazards associated to food before they become a health problem. The limitations of existing methods have encouraged the development of new technologies, among them biosensors. Success in biosensor design depends largely on the development of novel receptors with enhanced affinity to the target, while being stable and economical. Aptamers fulfill these characteristics, and thus have surfaced as promising alternatives to natural receptors. This Review describes analytical strategies developed so far using aptamers for the control of pathogens, allergens, adulterants, toxins and other forbidden contaminants to ensure food safety. The main progresses to date are presented, highlighting potential prospects for the future.
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Affiliation(s)
- Sonia Amaya-González
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, Oviedo 33006, Spain; E-Mails: (S.A.-G.); (N.S.-Á.); (A.J.M.-O.)
| | - Noemí de-los-Santos-Álvarez
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, Oviedo 33006, Spain; E-Mails: (S.A.-G.); (N.S.-Á.); (A.J.M.-O.)
| | - Arturo J. Miranda-Ordieres
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, Oviedo 33006, Spain; E-Mails: (S.A.-G.); (N.S.-Á.); (A.J.M.-O.)
| | - Maria Jesús Lobo-Castañón
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, Oviedo 33006, Spain; E-Mails: (S.A.-G.); (N.S.-Á.); (A.J.M.-O.)
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22
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Nucleic acid-based aptamers and their applications. NUCLEIC ACID-BASED DRUGS 2013. [DOI: 10.4155/ebo.13.405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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23
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Bruno JG. A review of therapeutic aptamer conjugates with emphasis on new approaches. Pharmaceuticals (Basel) 2013; 6:340-57. [PMID: 24276022 PMCID: PMC3816688 DOI: 10.3390/ph6030340] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 12/14/2022] Open
Abstract
The potential to emulate or enhance antibodies with nucleic acid aptamers while lowering costs has prompted development of new aptamer-protein, siRNA, drug, and nanoparticle conjugates. Specific focal points of this review discuss DNA aptamers covalently bound at their 3' ends to various proteins for enhanced stability and greater pharmacokinetic lifetimes in vivo. The proteins can include Fc tails of IgG for opsonization, and the first component of complement (C1q) to trigger complement-mediated lysis of antibiotic-resistant Gram negative bacteria, cancer cells and possibly some parasites during vulnerable stages. In addition, the 3' protein adduct may be a biotoxin, enzyme, or may simply be human serum albumin (HSA) or a drug known to bind HSA, thereby retarding kidney and other organ clearance and inhibiting serum exonucleases. In this review, the author summarizes existing therapeutic aptamer conjugate categories and describes his patented concept for PCR-based amplification of double-stranded aptamers followed by covalent attachment of proteins or other agents to the chemically vulnerable overhanging 3' adenine added by Taq polymerase. PCR amplification of aptamers could dramatically lower the current $2,000/gram cost of parallel chemical oligonucleotide synthesis, thereby enabling mass production of aptamer-3'-protein or drug conjugates to better compete against expensive humanized monoclonal antibodies.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 230, San Antonio, TX 78229, USA.
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Daprà J, Lauridsen LH, Nielsen AT, Rozlosnik N. Comparative study on aptamers as recognition elements for antibiotics in a label-free all-polymer biosensor. Biosens Bioelectron 2013; 43:315-20. [PMID: 23353009 DOI: 10.1016/j.bios.2012.12.058] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 02/07/2023]
Abstract
We present an all-polymer electrochemical microfluidic biosensor using Topas(®) as substrate and a conductive polymer bilayer as electrode material. The conductive bilayer consists of tosylate doped poly(3,4-ethylenedioxythiophene) (PEDOT:TsO) and the hydroxymethyl derivative PEDOT-OH:TsO, which was covalently functionalized with two aptamer probes with affinity to ampicillin or kanamycin A, respectively. Using electrochemical impedance spectroscopy (EIS) we were able to detect ampicillin in a concentration range from 100pM to 1μM and kanamycin A from 10nM to 1mM. The obtained EIS spectra were fitted with an equivalent circuit model successfully explaining the impedance signal. Real samples from regular ultra-high temperature treated low-fat milk spiked with ampicillin were successfully tested to assess the functionality of the sensor with real samples. In conclusion, we have demonstrated the applicability of the newly developed platform for real time, label-free and selective impedimetric detection of commonly used antibiotics. Additionally it was possible to detect ampicillin in a milk sample at a concentration below the allowed maximum residue limit (MRL) in the European Union.
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Affiliation(s)
- Johannes Daprà
- Department of Micro- and Nanotechnology, Technical University of Denmark, Produktionstorvet 423, DK-2800 Kgs. Lyngby, Denmark
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