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Economou A, Kokkinos C, Bousiakou L, Hianik T. Paper-Based Aptasensors: Working Principles, Detection Modes, and Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:7786. [PMID: 37765843 PMCID: PMC10536119 DOI: 10.3390/s23187786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Aptamers are short oligonucleotides designed to possess high binding affinity towards specific target compounds (ions, molecules, or cells). Due to their function and unique advantages, aptamers are considered viable alternatives to antibodies as biorecognition elements in bioassays and biosensors. On the other hand, paper-based devices (PADs) have emerged as a promising and powerful technology for the fabrication of low-cost analytical tools, mainly intended for on-site and point-of-care applications. The present work aims to provide a comprehensive overview of paper-based aptasensors. The review describes the fabrication methods and working principles of paper-based devices, the properties of aptamers as bioreceptors, the different modes of detection used in conjunction with aptasensing PADs, and representative applications for the detection of ions, small molecules, proteins, and cells. The future challenges and prospects of these devices are also discussed.
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Affiliation(s)
- Anastasios Economou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Christos Kokkinos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Leda Bousiakou
- IMD Laboratories Co., R&D Section, Lefkippos Technology Park, National Centre for Scientific Research (NCSR) Demokritos, Agia Paraskevi, P.O. Box 60037, 15130 Athens, Greece;
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 84248 Bratislava, Slovakia;
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de Sousa Lacerda CM, Almeida NBF, Dos Santos VCF, Plentz F, de Andrade ASR. Foot-and-mouth disease virus: DNA aptamer selection for the 3ABC protein. Virus Res 2023; 323:199008. [PMID: 36414190 PMCID: PMC10194325 DOI: 10.1016/j.virusres.2022.199008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/04/2022] [Accepted: 11/18/2022] [Indexed: 11/21/2022]
Abstract
Foot-and-mouth disease (FMD) is a devastating livestock disease caused by foot-and-mouth disease virus (FMDV), a member of the Picornaviridae family. The 3ABC is a non-structural protein of FMDV, produced during viral replication and absent from inactivated FMD vaccines. Nucleic acid aptamers are DNA or RNA oligonucleotides capable of binding with high specificity and affinity to a molecular target. The aim of this study was to obtain DNA aptamers specific for 3ABC protein with a view of their application in the FMD diagnosis. Aptamers are usually obtained through SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure. In this study, an aptamer (termed FMDV1) was selected by a variation of this technique called Capillary Electrophoresis SELEX (CE-SELEX). The FMDV1 aptamer showed high binding affinity to the 3ABC protein with Kd value in the nano molar range: 22.69 ± 1.79 nM. The FMDV1 aptamer binding to 3ABC was significantly higher when compared with the BSA protein, used as control, demonstrating its specificity.
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Affiliation(s)
- Camila Maria de Sousa Lacerda
- Centro de Desenvolvimento da Tecnologia Nuclear, CDTN, Belo Horizonte, MG 31270-901, Brasil; MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Belo Horizonte, MG, Brasil
| | - Nathalie Bonatti Franco Almeida
- Centro de Desenvolvimento da Tecnologia Nuclear, CDTN, Belo Horizonte, MG 31270-901, Brasil; MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Belo Horizonte, MG, Brasil
| | - Viviane Cristina Fernandes Dos Santos
- Centro de Desenvolvimento da Tecnologia Nuclear, CDTN, Belo Horizonte, MG 31270-901, Brasil; MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Belo Horizonte, MG, Brasil
| | - Flávio Plentz
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil; MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Belo Horizonte, MG, Brasil
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Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
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Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
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Almeida NBF, Sousa TASL, Santos VCF, Lacerda CMS, Silva TG, Grenfell RFQ, Plentz F, Andrade ASR. DNA aptamer selection and construction of an aptasensor based on graphene FETs for Zika virus NS1 protein detection. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2022; 13:873-881. [PMID: 36105684 PMCID: PMC9443353 DOI: 10.3762/bjnano.13.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne virus that is phylogenetically close to other medically important flaviviruses with high global public health significance, such as dengue (DENV) and yellow fever (YFV) viruses. Correct diagnosis of a flavivirus infection can be challenging, particularly in world regions where more than one flavivirus co-circulates and YFV vaccination is mandatory. Acid nucleic aptamers are oligonucleotides that bind to a specific target molecule with high affinity and specificity. Because of their unique characteristics, aptamers are promising tools for biosensor development. Aptamers are usually obtained through a procedure called "systematic evolution of ligands by exponential enrichment" (SELEX). In this study, we select an aptamer (termed ZIKV60) by capillary electrophoresis SELEX (CE-SELEX) to the Zika virus non-structural protein 1 (NS1) and counterselection against the NS1 proteins of DENV (serotypes 1, 2, 3, and 4) and YFV. The ZIKV60 dissociation constant (K d) is determined by enzyme-linked oligonucleotide assay (ELONA) and the aptamer specificity is evaluated by quantitative real-time polymerase chain reaction. ZIKV60 shows a high binding affinity to the ZIKV NS1 protein with a K d value of 2.28 ± 0.28 nM. The aptamer presents high specificity for ZIKV NS1 compared to NS1 of DENV and YFV. Furthermore, graphene field-effect transistor devices functionalized with ZIKV60 exhibit an evident identification of NS1 protein diluted in human serum. These results point to the applicability of biosensors based on the ZIKV60 aptamer for the differential diagnosis of the Zika virus.
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Affiliation(s)
- Nathalie B F Almeida
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
| | - Thiago A S L Sousa
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
- Current address: DTU Physics, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Viviane C F Santos
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
| | - Camila M S Lacerda
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
| | - Thais G Silva
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
| | - Rafaella F Q Grenfell
- Instituto René Rachou - Fundação Oswaldo Cruz, Avenida Augusto de Lima 1715, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Flavio Plentz
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
- MedicOnChip, Parque Tecnológico de Belo Horizonte-BH-TEC, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, CEP 31310-260, Brazil
| | - Antero S R Andrade
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Avenida Presidente Antônio Carlos 6627, Belo Horizonte, CEP 31270-901, Brazil
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A review on corona virus disease 2019 (COVID-19): current progress, clinical features and bioanalytical diagnostic methods. Mikrochim Acta 2022; 189:103. [PMID: 35157153 PMCID: PMC8852957 DOI: 10.1007/s00604-022-05167-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/11/2022] [Indexed: 01/08/2023]
Abstract
A new epidemic of acute respiratory viral pneumonia was discovered in central China at the end of 2019. The disease was given the name coronavirus disease 2019 (COVID-19), and the virus that caused this disease was known as severe acute respiratory syndrome coronavirus (SARS-CoV-2). So far, diagnostic methods have been focused on (a) human antibody detection, (b) viral antigen detection and (c) viral gene detection, the latter using RT-PCR being the most accurate approach. In this paper, we present a summary of the COVID-19 pandemic, clinical features and epidemiology and pathogenesis. Also, we focus on the recent advances in bioanalytical diagnostic methods based on various techniques for SARS-CoV-2 sensing that have recently been published (2020–2021). Furthermore, we present the mechanisms, advantages and disadvantages of the most common biosensors for COVID-19 detection, which include optical, electrochemical and piezoelectric biosensors as well as wearable and smart nanobiosensors, immunosensors, aptasensors and genosensors.
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Delaunay N, Combès A, Pichon V. Immunoaffinity Extraction and Alternative Approaches for the Analysis of Toxins in Environmental, Food or Biological Matrices. Toxins (Basel) 2020; 12:toxins12120795. [PMID: 33322240 PMCID: PMC7764248 DOI: 10.3390/toxins12120795] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
The evolution of instrumentation in terms of separation and detection allowed a real improvement of the sensitivity and analysis time. However, the analysis of ultra-traces of toxins in complex samples requires often a step of purification and even preconcentration before their chromatographic analysis. Therefore, immunoaffinity sorbents based on specific antibodies thus providing a molecular recognition mechanism appear as powerful tools for the selective extraction of a target molecule and its structural analogs to obtain more reliable and sensitive quantitative analysis in environmental, food or biological matrices. This review focuses on immunosorbents that have proven their efficiency in selectively extracting various types of toxins of various sizes (from small mycotoxins to large proteins) and physicochemical properties. Immunosorbents are now commercially available, and their use has been validated for numerous applications. The wide variety of samples to be analyzed, as well as extraction conditions and their impact on extraction yields, is discussed. In addition, their potential for purification and thus suppression of matrix effects, responsible for quantification problems especially in mass spectrometry, is presented. Due to their similar properties, molecularly imprinted polymers and aptamer-based sorbents that appear to be an interesting alternative to antibodies are also briefly addressed by comparing their potential with that of immunosorbents.
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Affiliation(s)
- Nathalie Delaunay
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), CBI ESPCI Paris, PSL University, CNRS, 75005 Paris, France; (N.D.); (A.C.)
| | - Audrey Combès
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), CBI ESPCI Paris, PSL University, CNRS, 75005 Paris, France; (N.D.); (A.C.)
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), CBI ESPCI Paris, PSL University, CNRS, 75005 Paris, France; (N.D.); (A.C.)
- Department of Chemistry, Sorbonne University, 75005 Paris, France
- Correspondence:
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Wu S, Liu Y, Sun H, Zhong M, Dai B, Pan B, Shen Z. An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins. Anal Biochem 2020; 607:113893. [PMID: 32739349 DOI: 10.1016/j.ab.2020.113893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/27/2022]
Abstract
Aptamers are small-sized RNA or ssDNA ligands with a unique structure, which have high specificity and affinity to their cognate targets. Thus, in addition to the extensive values in various bio-medical fields, aptamers can also be alternatively used as affinity ligands in the bioprocess, such as for protein purification. In the present study, a hexahistidine specific aptamer named AptHis-C, was developed through the SELEX methodology, which has high affinity to hexahistidine, and its dissociation constant was as low as 20.8 nM. The structural prediction revealed that AptHis-C contains two connected stem-loop conformations. AptHis-C can only specifically recognize recombinant proteins with the hexahistidine-tag in simple or complex situations, and not to those with other tags. When immobilized on magnetic beads, AptHis-C can be used as a tool for hexahistidine-tagged recombinant protein purification. Its effectiveness is as good as traditional Ni-based beads. Besides, due to the intrinsic characteristics of nucleic acids, such as high thermal/chemical stability, immobilized aptamer-magnetic beads can be reused many times without an obvious decrease of purification effectiveness. This aptamer may represent a novel method for the detection and purification of hexahistidine-tagged recombinant proteins.
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Affiliation(s)
- Shijia Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanting Liu
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China
| | - Hongguang Sun
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Meizuo Zhong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bichun Dai
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Biyao Pan
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhijian Shen
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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Miyagawa A, Okada Y, Okada T. Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field. ACS OMEGA 2020; 5:3542-3549. [PMID: 32118169 PMCID: PMC7045491 DOI: 10.1021/acsomega.9b03860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.
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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based immunoassay and aptamer assay: A review. Electrophoresis 2020; 41:414-433. [PMID: 31975407 DOI: 10.1002/elps.201900426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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An aptamer affinity column for purification and enrichment of aflatoxin B 1 and aflatoxin B 2 in agro-products. Anal Bioanal Chem 2020; 412:895-904. [PMID: 31900533 DOI: 10.1007/s00216-019-02300-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/04/2019] [Accepted: 11/22/2019] [Indexed: 01/20/2023]
Abstract
We have developed an aptamer affinity column (AAC) for the purification and enrichment of trace aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) in genuine agro-products through the covalent conjugation of amino modified aptamer and NHS-activated Sepharose. The coupling and working conditions found to be suitable for this AFB-AAC were examined in regard to coupling time (2 min), loading volume (30 mL), and the methanol concentration (< 10%) used in the loading step. The performance of AFB-AAC was then further evaluated in terms of capacity (329.1 ± 13.7 ng for AFB1 and 162.5 ± 8.9 ng for AFB2), selectivity (excellent), reusability (twenty-three times for AFB1 and twelve times for AFB2), and repeatability (92.7% ± 2.9% for AFB1 and 71.5% ± 3.4% for AFB2). Furthermore, the AAC clean-up combined with HPLC-FLD demonstrated excellent linearity over a wide range, good sensitivity with an LOD of 50 pg mL-1 for AFB1 and 15 pg mL-1 for AFB2, and acceptable recovery with different spiking levels in different matrices. Finally, the AAC was successfully applied to analyte AFB1 and AFB2 in four types of agro-products as well as a maize flour reference material, and the results were found to be in accordance with those of commercial IACs. This study provides a reference for the analysis of other trace analytes by merely changing the corresponding aptamer and represents a strong contender for immune affinity columns. Graphical abstract An aptamer affinity column for purification and enrichment of aflatoxin B1 and aflatoxin B2 in agro-products with the aid of HPLC-FLD and a post-column photochemical derivatization reactor.
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Ghassami E, Varshosaz J, Mirian M, Jahanian-Najafabadi A. HER-2 aptamer-targeted Ecoflex ® nanoparticles loaded with docetaxel promote breast cancer cells apoptosis and anti-metastatic effect. IET Nanobiotechnol 2019; 13:428-434. [PMID: 31171748 DOI: 10.1049/iet-nbt.2018.5047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Breast cancer is a major cause of cancer mortality. Regarding the advantages of polymeric nanoparticles as drug delivery systems with targeting potential, in this study the antitumor mechanism of targeted docetaxel polymeric nanoparticles of Ecoflex® was exploited. Since the overexpression of HER-2 receptor in breast cancer cases is associated with poor prognosis and more aggressive disease, the proposed nanoparticles were conjugated to HER-2 specific aptamer molecules. In vitro cytotoxicity was evaluated by MTT assay. Flow-cytometry analysis was performed to evaluate the cellular uptake of nanoparticles loaded with a fluorescent probe. Anti-migration effects of samples were studied. Annexin IV-FITC and propidium iodide were implemented to investigate apoptosis induction and cell cycle analysis. Enhanced cytotoxicity compared with free docetaxel was explained considering improved cellular uptake of the nanoparticles and induced apoptosis in a larger portion of cells. Lower relative migration demonstrated enhanced anti-migration effect of nanoparticles, and cell cycle was arrested in G2/M phase using both formulations so the anti-microtubule mechanism of the drug was not altered. Therefore, this system could offer a potential substitute for the currently marketed docetaxel formulations, which may reduce adverse effects of the drug, while further in vivo and clinical investigations are required.
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Affiliation(s)
- Erfaneh Ghassami
- Pharmacy Students Research Committee, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jaleh Varshosaz
- Department of Pharmaceutics, Faculty of Pharmacy and Novel Drug Delivery Systems Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
Stereospecific recognition of chiral molecules plays an important role in nature as the basis of the interaction of chiral bioactive compounds with the chiral target structures. In separation sciences such as chromatographic and capillary electromigration techniques, interactions between chiral analytes and chiral selectors, i.e., the formation of transient diastereomeric complexes in thermodynamic equilibria, are the basis for chiral separations. Due to the large structural variety of chiral selectors, different structural features contribute to the overall chiral recognition process. This introductory chapter briefly summarizes the present understanding of the structural enantioselective recognition processes for various types of chiral selectors.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical Chemistry, University of Jena, Jena, Germany.
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13
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Implementation of electrochemical impedance spectroscopy to evaluate HER-2 aptamer conjugation to Ecoflex® nanoparticles for docetaxel delivery in breast cancer cells. J APPL ELECTROCHEM 2018. [DOI: 10.1007/s10800-018-1273-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Carrasquilla C, Kapteyn E, Li Y, Brennan JD. Sol-Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers. Angew Chem Int Ed Engl 2017; 56:10686-10690. [PMID: 28556430 DOI: 10.1002/anie.201702859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Indexed: 11/10/2022]
Abstract
Sol-gel-derived bio/inorganic hybrid materials have been examined for diverse applications, including biosensing, affinity chromatography and drug discovery. However, such materials have mostly been restricted to the interaction between entrapped biorecognition elements and small molecules, owing to the requirement for nanometer-scale mesopores in the matrix to retain entrapped biorecognition elements. Herein, we report on a new class of macroporous bio/inorganic hybrids, engineered through a high-throughput materials screening approach, that entrap micron-sized concatemeric DNA aptamers. We demonstrate that the entrapment of these long-chain DNA aptamers allows their retention within the macropores of the silica material, so that aptamers can interact with high molecular weight targets such as proteins. Our approach overcomes the major limitation of previous sol-gel-derived biohybrid materials by enabling molecular recognition for targets beyond small molecules.
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Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - Emily Kapteyn
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - Yingfu Li
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - John D Brennan
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
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15
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Carrasquilla C, Kapteyn E, Li Y, Brennan JD. Sol-Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - Emily Kapteyn
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - Yingfu Li
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - John D. Brennan
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
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16
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Selective tools for the solid-phase extraction of Ochratoxin A from various complex samples: immunosorbents, oligosorbents, and molecularly imprinted polymers. Anal Bioanal Chem 2016; 408:6983-99. [PMID: 27585915 DOI: 10.1007/s00216-016-9886-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/21/2016] [Accepted: 08/16/2016] [Indexed: 12/27/2022]
Abstract
The evolution of instrumentation in terms of separation and detection has allowed a real improvement of the sensitivity and the analysis time. However, the analysis of ultra-traces of toxins such as ochratoxin A (OTA) from complex samples (foodstuffs, biological fluids…) still requires a step of purification and of preconcentration before chromatographic determination. In this context, extraction sorbents leading to a molecular recognition mechanism appear as powerful tools for the selective extraction of OTA and of its structural analogs in order to obtain more reliable and sensitive quantitative analyses of these compounds in complex media. Indeed, immunosorbents and oligosorbents that are based on the use of immobilized antibodies and of aptamers, respectively, and that are specific to OTA allow its selective clean-up from complex samples with high enrichment factors. Similar molecular recognition mechanisms can also be obtained by developing molecularly imprinted polymers, the synthesis of which leads to the formation of cavities that are specific to OTA, thus mimicking the recognition site of the biomolecules. Therefore, the principle, the advantages, the limits of these different types of extraction tools, and their complementary behaviors will be presented. The introduction of these selective tools in miniaturized devices will also be discussed.
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Ravalli A, Voccia D, Palchetti I, Marrazza G. Electrochemical, Electrochemiluminescence, and Photoelectrochemical Aptamer-Based Nanostructured Sensors for Biomarker Analysis. BIOSENSORS-BASEL 2016; 6:bios6030039. [PMID: 27490578 PMCID: PMC5039658 DOI: 10.3390/bios6030039] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/12/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022]
Abstract
Aptamer-based sensors have been intensively investigated as potential analytical tools in clinical analysis providing the desired portability, fast response, sensitivity, and specificity, in addition to lower cost and simplicity versus conventional methods. The aim of this review, without pretending to be exhaustive, is to give the readers an overview of recent important achievements about electrochemical, electrochemiluminescence, and photoelectrochemical aptasensors for the protein biomarker determination, mainly cancer related biomarkers, by selected recent publications. Special emphasis is placed on nanostructured-based aptasensors, which show a substantial improvement of the analytical performances.
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Affiliation(s)
- Andrea Ravalli
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
| | - Diego Voccia
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
| | - Ilaria Palchetti
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
| | - Giovanna Marrazza
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
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18
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Morschheuser L, Wessels H, Pille C, Fischer J, Hünniger T, Fischer M, Paschke-Kratzin A, Rohn S. HPTLC-aptastaining - Innovative protein detection system for high-performance thin-layer chromatography. Sci Rep 2016; 6:26665. [PMID: 27220270 PMCID: PMC4879557 DOI: 10.1038/srep26665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023] Open
Abstract
Protein analysis using high-performance thin-layer chromatography (HPTLC) is not commonly used but can complement traditional electrophoretic and mass spectrometric approaches in a unique way. Due to various detection protocols and possibilities for hyphenation, HPTLC protein analysis is a promising alternative for e.g., investigating posttranslational modifications. This study exemplarily focused on the investigation of lysozyme, an enzyme which is occurring in eggs and technologically added to foods and beverages such as wine. The detection of lysozyme is mandatory, as it might trigger allergenic reactions in sensitive individuals. To underline the advantages of HPTLC in protein analysis, the development of innovative, highly specific staining protocols leads to improved sensitivity for protein detection on HPTLC plates in comparison to universal protein derivatization reagents. This study aimed at developing a detection methodology for HPTLC separated proteins using aptamers. Due to their affinity and specificity towards a wide range of targets, an aptamer based staining procedure on HPTLC (HPTLC-aptastaining) will enable manifold analytical possibilities. Besides the proof of its applicability for the very first time, (i) aptamer-based staining of proteins is applicable on different stationary phase materials and (ii) furthermore, it can be used as an approach for a semi-quantitative estimation of protein concentrations.
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Affiliation(s)
- Lena Morschheuser
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Hauke Wessels
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Christina Pille
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Judith Fischer
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Tim Hünniger
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Markus Fischer
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Angelika Paschke-Kratzin
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
| | - Sascha Rohn
- University of Hamburg, Hamburg School of Food Science, Institute of Food Chemistry, Grindelallee 117, D-20146 Hamburg
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19
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Scriba GKE. Chiral recognition in separation science - an update. J Chromatogr A 2016; 1467:56-78. [PMID: 27318504 DOI: 10.1016/j.chroma.2016.05.061] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 12/26/2022]
Abstract
Stereospecific recognition of chiral molecules is an important issue in various aspects of life sciences and chemistry including analytical separation sciences. The basis of analytical enantioseparations is the formation of transient diastereomeric complexes driven by hydrogen bonds or ionic, ion-dipole, dipole-dipole, van der Waals as well as π-π interactions. Recently, halogen bonding was also described to contribute to selector-selectand complexation. Besides structure-separation relationships, spectroscopic techniques, especially NMR spectroscopy, as well as X-ray crystallography have contributed to the understanding of the structure of the diastereomeric complexes. Molecular modeling has provided the tool for the visualization of the structures. The present review highlights recent contributions to the understanding of the binding mechanism between chiral selectors and selectands in analytical enantioseparations dating between 2012 and early 2016 including polysaccharide derivatives, cyclodextrins, cyclofructans, macrocyclic glycopeptides, proteins, brush-type selectors, ion-exchangers, polymers, crown ethers, ligand-exchangers, molecular micelles, ionic liquids, metal-organic frameworks and nucleotide-derived selectors. A systematic compilation of all published literature on the various chiral selectors has not been attempted.
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Affiliation(s)
- Gerhard K E Scriba
- Friedrich Schiller University Jena, Department of Pharmaceutical/Medicinal Chemistry, Philosophenweg 14, 07743 Jena, Germany.
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20
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Aptamer-Based Fluorescence Assay for Detection of Isocarbophos and Profenofos. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60933-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Lamberti I, Scarano S, Esposito CL, Antoccia A, Antonini G, Tanzarella C, De Franciscis V, Minunni M. In vitro selection of RNA aptamers against CA125 tumor marker in ovarian cancer and its study by optical biosensing. Methods 2015; 97:58-68. [PMID: 26542762 DOI: 10.1016/j.ymeth.2015.10.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/09/2015] [Accepted: 10/31/2015] [Indexed: 12/12/2022] Open
Abstract
Early identification of neoplastic diseases is essential to achieve timely therapeutic interventions and significantly reduce the mortality of patients. A well-known biomarker is the Cancer Antigen 125 (CA125) or 16 mucin (MUC 16), a glycoprotein of the human family of mucins, already used for the diagnostic and prognostic evaluation of ovarian cancer. Therefore, the detection of CA125 to now remains a promising tool in the early diagnosis of this tumor. In this paper, we describe the development of RNA aptamers that bind with high affinity the tumor antigen CA125. We performed eight cycles of selection against CA125 purified protein. The selected aptamers were cloned and sequenced and the binding properties of the most promising sequences were studied by Real Time PCR and Surface Plasmon Resonance (SPR) to evaluate their ability in targeting CA125 protein with perspective applications in aptamer-based bioassays.
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Affiliation(s)
- Ilaria Lamberti
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy
| | - Simona Scarano
- Università di Firenze, Dipartimento di Chimica "Ugo Schiff", Via della Lastruccia, 3-13, 50019 Sesto F.no (FI), Italy
| | - Carla Lucia Esposito
- Consiglio Nazionale delle Ricerche, Istituto per l'Endocrinologia e Oncologia Molecolare "G. Salvatore", Via T. De Amicis 95, 80131 Napoli, Italy
| | - Antonio Antoccia
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy; INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy
| | - Giovanni Antonini
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy; INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy
| | - Caterina Tanzarella
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy
| | - Vittorio De Franciscis
- Consiglio Nazionale delle Ricerche, Istituto per l'Endocrinologia e Oncologia Molecolare "G. Salvatore", Via T. De Amicis 95, 80131 Napoli, Italy.
| | - Maria Minunni
- INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy; Università di Firenze, Dipartimento di Chimica "Ugo Schiff", Via della Lastruccia, 3-13, 50019 Sesto F.no (FI), Italy.
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22
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Acquah C, Danquah MK, Yon JLS, Sidhu A, Ongkudon CM. A review on immobilised aptamers for high throughput biomolecular detection and screening. Anal Chim Acta 2015; 888:10-8. [PMID: 26320953 DOI: 10.1016/j.aca.2015.05.050] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 02/07/2023]
Abstract
The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.
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Affiliation(s)
- Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Michael K Danquah
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia.
| | - John L S Yon
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Amandeep Sidhu
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Faculty of Health Sciences, Curtin University, Perth, 6109, Australia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
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23
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Wang S, Liu J, Dong Y, Su H, Tan T. Conformational structure-dependent molecular recognition of two aptamers for tetracycline. RSC Adv 2015. [DOI: 10.1039/c5ra08050a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Base sequence, strand length, and number of recognition sites codetermine conformational structure and performance of aptamers for tetracycline recognition.
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Affiliation(s)
- Sai Wang
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Jiahui Liu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Yiyang Dong
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
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24
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Hagiwara K, Fujita H, Kasahara Y, Irisawa Y, Obika S, Kuwahara M. In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids. MOLECULAR BIOSYSTEMS 2014; 11:71-6. [PMID: 25325213 DOI: 10.1039/c4mb00436a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We successfully generated chimeric DNA aptamers that contained six nucleoside analogs of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) in the primer region and multiple guanosine analogs of 2'-deoxy-2'-fluoro-ribonucleic acid (FNA) in the non-primer region using capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX). Active species enrichment became saturated only after five selection rounds, and we obtained DNA-based xeno-nucleic acid (XNA) aptamers that had high binding affinities for the target human thrombin, with dissociation constant (Kd) values of ≥10 nanomolar. Based on sequence and circular dichroism (CD) analyses, these XNA aptamers exhibited RNA-like conformations, which could cause DNA-based strands to adopt structurally diverse conformations.
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Affiliation(s)
- Kenta Hagiwara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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25
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Aptamer-based-sorbents for sample treatment--a review. Anal Bioanal Chem 2014; 407:681-98. [PMID: 25286873 DOI: 10.1007/s00216-014-8129-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
To improve selectivity during sample pretreatment, various selective tools inducing a molecular recognition mechanism during the extraction procedure have been developed, such as sorbents constituted of immobilized antibodies, i.e., immunosorbents, or molecularly imprinted polymers. More recently, as an alternative to both previous approaches, aptamers immobilized onto a solid support, i.e., oligosorbents, were proposed. Thanks to the high affinity and high selectivity of the interaction that some aptamers offer toward some target analytes, they also provide powerful techniques that make selective extraction and the concentration of a target analyte from liquid matrices in one step or sample purification of extracts from solid matrices possible. This review describes the development and the properties of these oligosorbents developed for different types of targets-pharmaceuticals, mycotoxins, proteins, cells, etc. After describing the immobilization procedures, we discuss different parameters characterizing the potential of aptamer-based supports as extraction sorbents. Close relations exist between extraction recoveries and the affinity and amounts of aptamers immobilized on the extraction device. In addition, analyte-aptamer interactions may be affected by matrix components and by additives in the samples. This may also lower extraction recoveries and affect the stability and the possible reusability of the aptamer-based sorbent. All these points are discussed and illustrated. Numerous examples of applications of these sorbents to the treatment of complex samples such as food samples, environmental samples, and biological fluids are also reported. Their association with analytical devices, from conventional to miniaturized analytical systems, is also discussed.
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26
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Yang X, Kong W, Hu Y, Yang M, Huang L, Zhao M, Ouyang Z. Aptamer-affinity column clean-up coupled with ultra high performance liquid chromatography and fluorescence detection for the rapid determination of ochratoxin A in ginger powder. J Sep Sci 2014; 37:853-60. [PMID: 24482395 DOI: 10.1002/jssc.201301136] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/15/2014] [Accepted: 01/19/2014] [Indexed: 12/11/2022]
Abstract
Aptamers are single-stranded oligonucleotides with high affinity and specificity and are widely used in targets separation and enrichment. Here, an aptamer-affinity column (AAC) was firstly prepared in-house through a covalent immobilization strategy. Then, ochratoxin A (OTA) in ginger powder was absorbed and enriched using the new aptamer-based clean-up technology for the first time, and was further analyzed by ultra high performance liquid chromatography with fluorescence detection. After optimization, the average recoveries for blank samples spiked with OTA at 5, 15, and 45 μg/kg ranged from 85.36 to 96.83%. Furthermore, the AAC exhibited a similar accuracy as an immunoaffinity column to clean up OTA in ginger powder. Above all, it exhibited better reusability, twice that of the immunoaffinity column, had lower toxicity and cost, and took less time. Of 25 contaminated ginger powder samples, OTA contamination levels ranged from 1.51 to 4.31 μg/kg, which were lower than the European Union (EU) regulatory limits. All the positive samples were further confirmed by ultra-fast LC with MS/MS. In conclusion, the method of clean-up based on the AAC coupled to ultra-HPLC with fluorescence detection was rapid, specific, and sensitive for the quantitative analysis of OTA in a complex matrix.
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Affiliation(s)
- Xihui Yang
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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27
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Fu Y, Wang X, Zhang J, Li W. Nanomaterials and nanoclusters based on DNA modulation. Curr Opin Biotechnol 2013; 28:33-8. [PMID: 24832072 DOI: 10.1016/j.copbio.2013.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/31/2013] [Indexed: 12/27/2022]
Abstract
Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson-Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA self-assembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation.
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Affiliation(s)
- Yan Fu
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xian Wang
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jinli Zhang
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Wei Li
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China.
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28
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Šmuc T, Ahn IY, Ulrich H. Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics. J Pharm Biomed Anal 2013; 81-82:210-7. [PMID: 23666257 DOI: 10.1016/j.jpba.2013.03.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/11/2013] [Accepted: 03/20/2013] [Indexed: 02/07/2023]
Abstract
Aptamers are small nucleic acid molecules capable of binding to a wide range of target molecules with high affinity and specificity. They have been developed and widely used not only as research tools, but also as biosensors, specific antagonists, and diagnostic markers and as protein purification platform for many pharmaceutical and clinical applications. Here, in this paper we will explore biochemical aspects of aptamer-target interactions and show why aptamers rival antibodies in target recognition and purification procedures. This review will focus on strategies of using aptamers as affinity ligands for molecules of therapeutic and pharmaceutical interest including applications in chromatography and capillary electrophoresis for protein and small molecule purification. Moreover, we will also discuss aptamers whose binding parameters can be controlled on demand for diagnostic approaches and used as sensitive receptors in biosensorics. Aptamers have opened up exciting fields in basic and applied research of pharmaceutical and biotechnological interest.
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Affiliation(s)
- Tina Šmuc
- Laboratory for Bio-instrumentation, Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
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29
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Abstract
Chiral recognition phenomena play an important role in nature as well as analytical separation sciences. In separation sciences such as chromatography and capillary electrophoresis, enantiospecific interactions between the enantiomers of an analyte and the chiral selector are required in order to observe enantioseparations. Due to the large structural variety of chiral selectors applied, different mechanisms and structural features contribute to the chiral recognition process. This chapter briefly illustrates the current models of the enantiospecific recognition on the structural basics of various chiral selectors.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Jena, Germany.
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30
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Abstract
Capillary electrophoresis (CE) has matured to one of the major liquid phase enantiodifferentiation techniques since the first report in 1985. This can be primarily attributed to the flexibility as well as the various modes available including electrokinetic chromatography (EKC), micellar electrokinetic chromatography (MEKC), and microemulsion electrokinetic chromatography (MEEKC). In contrast to chromatographic techniques, the chiral selector is mobile in the background electrolyte. Furthermore, a large variety of chiral selectors are available that can be easily combined in the same separation system. In addition, the migration order of the enantiomers can be adjusted by a number of approaches. In CE enantiodifferentiations the separation principle is comparable to chromatography while the principle of the movement of the analytes in the capillary is based on electrophoretic phenomena. The present chapter will focus on mechanistic aspects of CE enantioseparations including enantiomer migration order and the current understanding of selector-selectand structures. Selected examples of the basic enantioseparation modes EKC, MEKC, and MEEKC will be discussed.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Philosophenweg 14, 07743, Jena, Germany,
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Zhou P, Luo Q, Lin Y, Chen L, Li S, Zhou G, Ji X, He Z. Immunoassays with protein misfolding cycle amplification: a platform for ultrasensitive detection of antigen. Anal Chem 2012; 84:7343-9. [PMID: 22888831 DOI: 10.1021/ac300805u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein misfolding cycle amplification (PMCA), a novel technology on amplifying cyclically misfolded proteins in vitro, is conceptually analogous to DNA amplification by polymerase chain reaction (PCR) and has tremendous implications for the researches and diagnosis. Here we first introduce the protein amplification technology into the classic immunoassay and develop a PMCA-based immunoassay (immuno-PMCA) for highly sensitive detection of antigen. This method takes advantage of sandwich binding of two affinity aptamers for increased specificity, magnetic nanoparticles for fast magnetic separation, PMCA for signal amplification, and conjugated polyelectrolytes for visual detection, allowing the detection limit of antigen by colorimetry down to femtomolar level with a wide linear range from 10 to 10(4) fM. More importantly, no specialized facilities or enzymes are needed either in the amplification reaction or the evaluation of results, which indicates its great potential application in immunological research and clinical diagnostics.
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
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Walter JG, Stahl F, Scheper T. Aptamers as affinity ligands for downstream processing. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100197] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Johanna-Gabriela Walter
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Frank Stahl
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Thomas Scheper
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
| | - Lianghai Hu
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
| | - W. Andy Tao
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
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Hu X, Mu L, Zhou Q, Wen J, Pawliszyn J. ssDNA aptamer-based column for simultaneous removal of nanogram per liter level of illicit and analgesic pharmaceuticals in drinking water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:4890-4895. [PMID: 21539347 DOI: 10.1021/es104241z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Aptamers are a new class of single-stranded DNA/RNA molecules selected from synthetic nucleic acid libraries for molecular recognition. Our group reports a novel aptamer column for the removal of trace (ng/L) pharmaceuticals in drinking water. In this study, cocaine and diclofenac were chosen as model molecules to test the aptamer column which presented high removal capacity, selectivity, and stability. The removal of pharmaceuticals was as high as 88-95%. The data of adsorption were fitted with Langmuir isotherm and a pseudo-second-order kinetic model. A thermodynamic experiment proved the adsorption processes were exothermic in spontaneity. The kinetics of aptamer was composed of three steps: activation, binding, and hybridization. The first step was the rate-controlling step. The adsorption system was divided into three parts: kinetic, mixed, and thermodynamic zones from 0% to 100% binding fraction of aptamer. Furthermore, the aptamer column was reusable and achieved strong removal efficiency from 4 to 30 °C at normal cation ion concentration (5-100 mg/L) for multipollutants without cross effects and secondary pollution. This work indicates that aptamer, as a new sorbent, can be used in the removal of persistent organic pollutants, biological toxins, and pathogenic bacteria from surface, drinking, and ground water.
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Affiliation(s)
- Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
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Arrua RD, Alvarez Igarzabal CI. Macroporous monolithic supports for affinity chromatography. J Sep Sci 2011; 34:1974-87. [DOI: 10.1002/jssc.201100197] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 01/21/2023]
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Baqué M, Le Postollec A, Ravelet C, Peyrin E, Coussot G, Desvignes I, Incerti S, Moretto P, Dobrijevic M, Vandenabeele-Trambouze O. Investigation of low-energy proton effects on aptamer performance for astrobiological applications. ASTROBIOLOGY 2011; 11:207-211. [PMID: 21434764 DOI: 10.1089/ast.2010.0520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biochips are promising instruments for the search for organic molecules in planetary environments. Nucleic acid aptamers are powerful affinity receptors known for their high affinity and specificity, and therefore are of great interest for space biochip development. A wide variety of aptamers have already been selected toward targets of astrobiological interest (from amino acids to microorganisms). We present a first study to test the resistance of these receptors to the constraints of the space environment. The emphasis is on the effect of cosmic rays on the molecular recognition properties of DNA aptamers. Experiments on beam-line facilities have been conducted with 2 MeV protons and fluences much higher than expected for a typical mission to Mars. Our results show that this irradiation process did not affect the performances of DNA aptamers as molecular recognition tools.
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Affiliation(s)
- M Baqué
- Institut des Biomolécules Max Mousseron-IBMM, Centre National de la Recherche Scientifique, Université de Montpellier, Unité Mixte de Recherche, France
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New extraction sorbent based on aptamers for the determination of ochratoxin A in red wine. Anal Bioanal Chem 2011; 400:1199-207. [PMID: 21221554 DOI: 10.1007/s00216-010-4574-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 11/26/2010] [Accepted: 11/29/2010] [Indexed: 10/18/2022]
Abstract
A new solid phase extraction method based on aptamers, an oligosorbent, was developed and applied to the determination of ochratoxin A (OTA) from red wine. Two solid supports were chosen to immobilize OTA aptamer by covalent binding (cyanogen bromide-activated sepharose) or noncovalent binding (streptavidin-activated agarose). The resulting oligosorbents were evaluated in terms of retention, selectivity, and capacity. To assess the selectivity of the resulting oligosorbents, control supports made only of a solid support without immobilized aptamers were simultaneously studied. After optimization of the selective extraction procedure, extraction recoveries close to 100% were obtained on both materials. No retention was observed on the control supports. A similar capacity was also found for both oligosorbents. However, the immobilization by covalent bonding appeared more robust for the determination of OTA in the wine. A conventional sorbent and an immunoaffinity column were also applied to the determination of OTA in red wine to compare the potential of the various approaches for the treatment of such complex samples.
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Automation in the high-throughput selection of random combinatorial libraries--different approaches for select applications. Molecules 2010; 15:2478-90. [PMID: 20428057 PMCID: PMC6257267 DOI: 10.3390/molecules15042478] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/30/2010] [Accepted: 04/06/2010] [Indexed: 11/30/2022] Open
Abstract
Automation in combination with high throughput screening methods has revolutionised molecular biology in the last two decades. Today, many combinatorial libraries as well as several systems for automation are available. Depending on scope, budget and time, a different combination of library and experimental handling might be most effective. In this review we will discuss several concepts of combinatorial libraries and provide information as what to expect from these depending on the given context.
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