1
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Zheng M, Ye J, Liu H, Wu Y, Shi Y, Xie Y, Wang S. FAM Tag Size Separation-Based Capture-Systematic Evolution of Ligands by Exponential Enrichment for Sterigmatocystin-Binding Aptamers with High Specificity. Anal Chem 2024; 96:710-720. [PMID: 38175632 DOI: 10.1021/acs.analchem.3c03675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sterigmatocystin (ST) is a known toxin whose aptamer has rarely been reported because ST is a water-insoluble small-molecule target with few active sites, leading to difficulty in obtaining its aptamer using traditional target fixation screening methods. To obtain aptamer for ST, we incorporated FAM tag size separation into the capture-systematic evolution of ligands by exponential enrichment and combined it with molecular activation for aptamer screening. The screening process was monitored using a quantitative polymerase chain reaction fluorescence amplification curve and recovery of negative-, counter-, and positive-selected ssDNA. The affinity and specificity of the aptamer were verified by constructing an aptamer-affinity column, and the binding sites were predicted using molecular docking simulations. The results showed that the Kd value of the H Seq02 aptamer was 25.3 nM. The aptamer-affinity column based on 2.3 nmol of H Seq02 exhibited a capacity of about 80 ng, demonstrating better specificity than commercially available antibody affinity columns. Molecular simulation docking predicted the binding sites for H Seq02 and ST, further explaining the improved specificity. In addition, circular dichroism and isothermal titration calorimetry were used to verify the interaction between the aptamer and target ST. This study lays the foundation for the development of a new ST detection method.
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Affiliation(s)
- Mengyao Zheng
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Jin Ye
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hongmei Liu
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Yu Wu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yakun Shi
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Yanli Xie
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Songxue Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
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2
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Banu K, Mondal B, Rai B, Monica N, Hanumegowda R. Prospects for the application of aptamer based assay platforms in pathogen detection. Biocybern Biomed Eng 2022. [DOI: 10.1016/j.bbe.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Miller AA, Rao AS, Nelakanti SR, Kujalowicz C, Shi T, Rodriguez T, Ellington AD, Stovall GM. Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations. Anal Chem 2022; 94:7731-7737. [PMID: 35420426 PMCID: PMC9179646 DOI: 10.1021/acs.analchem.1c04407] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aptamers have been the subject of more than 144 000 papers to date. However, there has been a growing concern that discrepancies in the reporting of aptamer research limit the reliability of these reagents for research and other applications. These observations noting inconsistencies in the use of our RNA antilysozyme aptamer served as an impetus for our systematic review of the reporting of aptamer sequences in the literature. Our detailed examination of the literature citing the RNA antilysozyme aptamer revealed that 93% of the 61 publications reviewed reported unexplained altered sequences with 96% of those using DNA variants. The 10 most cited aptamers were examined using a standardized methodology in order to categorize the extent to which the sequences themselves and altered sequences were adequately described in the literature. Our review of 780 aptamer publications spanned decades, multiple journals, and research groups and revealed that 41% of the papers reported unexplained sequence alterations or omitted sequences. We identified 10 common categories of sequence alterations including deletions, substitutions, and additions, among others. Overall, our findings can be used as a starting point for building better practices in author submissions and publication standards, elevating the rigor and reproducibility of aptamer research.
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Affiliation(s)
- Alexandra A Miller
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Abhijit S Rao
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sujana R Nelakanti
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Kujalowicz
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted Shi
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted Rodriguez
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D Ellington
- Institute for Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Gwendolyn M Stovall
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States.,Texas Institute for Discovery Education in Science High School Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Zhao M, Wang M, Zhang X, Zhu Y, Cao J, She Y, Cao Z, Li G, Wang J, Abd El-Aty AM. Recognition elements based on the molecular biological techniques for detecting pesticides in food: A review. Crit Rev Food Sci Nutr 2021:1-24. [PMID: 34852703 DOI: 10.1080/10408398.2021.2009762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Excessive use of pesticides can cause contamination of the environment and agricultural products that are directly threatening human life and health. Therefore, in the process of food safety supervision, it is crucial to conduct sensitive and rapid detection of pesticide residues. The recognition element is the vital component of sensors and methods for fast testing pesticide residues in food. Improper recognition elements may lead to defects of testing methods, such as poor stability, low sensitivity, high economic costs, and waste of time. We can use the molecular biological technique to address these challenges as a good strategy for recognition element production and modification. Herein, we review the molecular biological methods of five specific recognition elements, including aptamers, genetic engineering antibodies, DNAzymes, genetically engineered enzymes, and whole-cell-based biosensors. In addition, the application of these identification elements combined with biosensor and immunoassay methods in actual detection was also discussed. The purpose of this review was to provide a valuable reference for further development of rapid detection methods for pesticide residues.
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Affiliation(s)
- Mingqi Zhao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Miao Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Xiaoguang Zhang
- Hebei Xiangzhi Testing Technology Co., Ltd, Shijiazhuang, China.,Core Facilities and Centers of Hebei Medical University, Shijiazhuang, China
| | - Yongan Zhu
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Jing Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Yongxin She
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Zhen Cao
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Institute of Quality Standardization & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agrofood Safety and Quality (Beijing), Ministry of Agriculture and Rural Areas, Beijing, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.,Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum, Turkey
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5
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Norouz Dizaji A, Simsek Ozek N, Aysin F, Calis A, Yilmaz A, Yilmaz M. Combining vancomycin-modified gold nanorod arrays and colloidal nanoparticles as a sandwich model for the discrimination of Gram-positive bacteria and their detection via surface-enhanced Raman spectroscopy (SERS). Analyst 2021; 146:3642-3653. [DOI: 10.1039/d1an00321f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study reports the development of a highly sensitive antibiotic-based discrimination and sensor platform for the detection of Gram-positive bacteria through surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Araz Norouz Dizaji
- East Anatolia High Technology Application and Research Center (DAYTAM)
- Ataturk University
- 25240 Erzurum
- Turkey
- Department of Chemical Engineering
| | - Nihal Simsek Ozek
- East Anatolia High Technology Application and Research Center (DAYTAM)
- Ataturk University
- 25240 Erzurum
- Turkey
- Department of Biology
| | - Ferhunde Aysin
- East Anatolia High Technology Application and Research Center (DAYTAM)
- Ataturk University
- 25240 Erzurum
- Turkey
- Department of Biology
| | - Ayfer Calis
- Department of Genetics and Bioengineering
- Giresun University
- 28200 Giresun
- Turkey
| | - Asli Yilmaz
- East Anatolia High Technology Application and Research Center (DAYTAM)
- Ataturk University
- 25240 Erzurum
- Turkey
- Department of Molecular Biology and Genetics
| | - Mehmet Yilmaz
- East Anatolia High Technology Application and Research Center (DAYTAM)
- Ataturk University
- 25240 Erzurum
- Turkey
- Department of Chemical Engineering
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6
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He M, Shang N, Zhu Q, Xu J. Paper-based upconversion fluorescence aptasensor for the quantitative detection of immunoglobulin E in human serum. Anal Chim Acta 2020; 1143:93-100. [PMID: 33384135 DOI: 10.1016/j.aca.2020.11.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Immunoglobulin E (IgE), a biomarker of allergic diseases, plays a critical role in allergic mechanism. Because of its low abundance in serum, the demand of developing sensitive, selective and simple methods for IgE detection is still very urgent. Paper-based analytical devices using upconversion nanoparticles (UCNPs) as the label can be promising point-of-care test (POCT) methods in rapid diagnosis, owing to their NIR-excitation and visible light emission nature, which can avoid the interference of autofluorescence and scattering light from biological samples and paper substrates. In this work, we proposed a paper-based analytical device for the sensitive, selective and accurate detection of total immunoglobulin E (IgE) in human serum. The assay was based on resonance energy transfer between UCNPs and organic dye tetramethylrhodamine (TAMRA), and IgE aptamer with stem-loop structure was used as the recognizing probe. The existence of IgE change the conformation of IgE aptamer, enlarge the distance between donor and acceptor, and block the energy transfer process. Thus, the luminescence of UCNPs recovered with an IgE concentration independent manner. A linear calibration was obtained in the range of 0.5-50 IU/mL, with a detection limit of 0.13 IU/mL. The results of our method were well correlated with that of commercial ELISA kit (20 human serum samples). This work suggests promising prospect of the paper-based UC-LRET analytical devices in real samples and may promote the application of paper-based analytical devices in clinical diagnosis.
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Affiliation(s)
- Mengyuan He
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, 464000, China.
| | - Ning Shang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, 464000, China
| | - Qianru Zhu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, 464000, China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, 464000, China
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7
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Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus. SENSORS 2020; 20:s20174977. [PMID: 32887407 PMCID: PMC7506613 DOI: 10.3390/s20174977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/29/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.
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8
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Bognár Z, Gyurcsányi RE. Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications. Int J Mol Sci 2020; 21:E5748. [PMID: 32796581 PMCID: PMC7461046 DOI: 10.3390/ijms21165748] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets-IgA, IgM, IgG and IgE-have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.
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Affiliation(s)
| | - Róbert E. Gyurcsányi
- 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;
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9
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Gulati P, Mishra P, Khanuja M, Narang J, Islam S. Nano-moles detection of tumor specific biomarker DNA for colorectal cancer detection using vertically aligned multi-wall carbon nanotubes based flexible electrodes. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Lietard J, Somoza MM. Spotting, Transcription and In Situ Synthesis: Three Routes for the Fabrication of RNA Microarrays. Comput Struct Biotechnol J 2019; 17:862-868. [PMID: 31321002 PMCID: PMC6612525 DOI: 10.1016/j.csbj.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022] Open
Abstract
DNA microarrays have become commonplace in the last two decades, but the synthesis of other nucleic acids biochips, most importantly RNA, has only recently been developed to a similar extent. RNA microarrays can be seen as organized surfaces displaying a potentially very large number of unique sequences and are of invaluable help in understanding the complexity of RNA structure and function as they allow the probing and treatment of each of the many different sequences simultaneously. Three approaches have emerged for the fabrication of RNA microarrays. The earliest examples used a direct, manual or mechanical, deposition of pre-synthesized, purified RNA oligonucleotides onto the surface in a process called spotting. In a second approach, pre-spotted or in situ-synthesized DNA microarrays are employed as templates for the transcription of RNA, subsequently or immediately captured on the surface. Finally, a third approach attempts to mirror the phosphoramidite-based protocols for in situ synthesis of high-density DNA arrays in order to produce in situ synthesized RNA microarrays. In this mini-review, we describe the chemistry and the engineering behind the fabrications methods, underlining the advantages and shortcomings of each, and illustrate how versatile these platforms can be by presenting some of their applications.
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11
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Awang T, Thangsan P, Luksirikul P, Japrung D, Pongprayoon P. The adsorption of glycated human serum albumin-selective aptamer onto a graphene sheet: simulation studies. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1605599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tadsanee Awang
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Thailand
| | - Poomsith Thangsan
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Thailand
| | - Patraporn Luksirikul
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Thailand
| | - Deanpen Japrung
- National Science and Technology Development Agency, National Nanotechnology Center, Thailand Science Park, Pathumthani, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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12
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Lietard J, Ameur D, Damha MJ, Somoza MM. High-Density RNA Microarrays Synthesized In Situ by Photolithography. Angew Chem Int Ed Engl 2018; 57:15257-15261. [PMID: 30187993 PMCID: PMC6237118 DOI: 10.1002/anie.201806895] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Indexed: 02/03/2023]
Abstract
While high-density DNA microarrays have been available for over three decades, the synthesis of equivalent RNA microarrays has proven intractable until now. Herein we describe the first in situ synthesis of mixed-based, high-density RNA microarrays using photolithography and light-sensitive RNA phosphoramidites. With coupling efficiencies comparable to those of DNA monomers, RNA oligonucleotides at least 30 nucleotides long can now efficiently be prepared using modified phosphoramidite chemistry. A two-step deprotection route unmasks the phosphodiester, the exocyclic amines and the 2' hydroxyl. Hybridization and enzymatic assays validate the quality and the identity of the surface-bound RNA. We show that high-density is feasible by synthesizing a complex RNA permutation library with 262144 unique sequences. We also introduce DNA/RNA chimeric microarrays and explore their applications by mapping the sequence specificity of RNase HII.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Dominik Ameur
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Rue Sherbrooke OMontréalQC H3A 0B8Canada
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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13
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Lietard J, Ameur D, Damha MJ, Somoza MM. In‐situ‐Synthese von hochdichten RNA‐Mikroarrays mittels Photolithographie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jory Lietard
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Dominik Ameur
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Masad J. Damha
- Department of ChemistryMcGill University 801 Rue Sherbrooke O Montréal QC H3A 0B8 Kanada
| | - Mark M. Somoza
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
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14
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Gating Hysteresis as an Indicator for Silicon Nanowire FET Biosensors. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8060950] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Zhang Z, Liu C, Yang C, Wu Y, Yu F, Chen Y, Du J. Aptamer-Patterned Hydrogel Films for Spatiotemporally Programmable Capture and Release of Multiple Proteins. ACS APPLIED MATERIALS & INTERFACES 2018; 10:8546-8554. [PMID: 29465230 DOI: 10.1021/acsami.8b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Various hydrogels have been used for protein delivery in the treatment of human diseases. Nevertheless, it is always difficult to control the capture and release of multiple proteins in different regions and periods. This research successfully proves that multiple proteins can be captured and released from the aptamer-patterned hydrogel films with an adjustable release rate at a prospective time and in specific regions utilizing the complementary DNA strand of aptamers via photoclick chemistry and DNA hybridization. The hydrogel film is successfully applied to complex matrixes such as human serum and has excellent cytocompatibility. Thus, the aptamer-patterned hydrogel film will be a good candidate for controlled delivery of multiple proteins.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Chen Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Chunzheng Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Yuyang Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Feng Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Yong Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Jie Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
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16
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Abstract
Biomarkers are at the cornerstone of preventive measures and contribute to the screening process. More recently, biomarkers have been used to gauge the biological response to the employed therapies. Since it is ubiquitously used to detect subclinical disease process, biomarkers also have found its place in cancer therapy related cardiac dysfunction (CTRCD). The aim of this review is to comprehensively present up-to-date knowledge of biomarkers in CTRCD and highlight some of the future biomedical technologies that may strengthen the screening process, and/or provide new insight in pathological mechanisms behind CTRCD.
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Affiliation(s)
- Rohit Moudgil
- Division of Cardiology, MD Anderson Cancer Center, 1515 W Holcombe Blvd, Houston, TX, 77030, USA.
| | - Parag A Parekh
- Department of Endocrine Neoplasia and Hormonal Disorders, MD Anderson Cancer Center, Houston, USA
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17
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Peltomaa R, Benito-Peña E, Barderas R, Sauer U, González Andrade M, Moreno-Bondi MC. Microarray-Based Immunoassay with Synthetic Mimotopes for the Detection of Fumonisin B1. Anal Chem 2017; 89:6216-6223. [DOI: 10.1021/acs.analchem.7b01178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Ursula Sauer
- Center
for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Martin González Andrade
- Department
of Biochemistry, Faculty of Medicine, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán D.F., México
City 04510, México
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18
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Ruan M, Seydou M, Noel V, Piro B, Maurel F, Barbault F. Molecular Dynamics Simulation of a RNA Aptasensor. J Phys Chem B 2017; 121:4071-4080. [PMID: 28363022 DOI: 10.1021/acs.jpcb.6b12544] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
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Affiliation(s)
- Min Ruan
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France.,School of Materials and Metallurgy, Hubei Polytechnic University , Huangshi, Hubei, China
| | - Mahamadou Seydou
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Vincent Noel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Benoit Piro
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - François Maurel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Florent Barbault
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
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19
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Vasilescu A, Nunes G, Hayat A, Latif U, Marty JL. Electrochemical Affinity Biosensors Based on Disposable Screen-Printed Electrodes for Detection of Food Allergens. SENSORS (BASEL, SWITZERLAND) 2016; 16:E1863. [PMID: 27827963 PMCID: PMC5134522 DOI: 10.3390/s16111863] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 01/04/2023]
Abstract
Food allergens are proteins from nuts and tree nuts, fish, shellfish, wheat, soy, eggs or milk which trigger severe adverse reactions in the human body, involving IgE-type antibodies. Sensitive detection of allergens in a large variety of food matrices has become increasingly important considering the emergence of functional foods and new food manufacturing technologies. For example, proteins such as casein from milk or lysozyme and ovalbumin from eggs are sometimes used as fining agents in the wine industry. Nonetheless, allergen detection in processed foods is a challenging endeavor, as allergen proteins are degraded during food processing steps involving heating or fermentation. Detection of food allergens was primarily achieved via Enzyme-Linked Immuno Assay (ELISA) or by chromatographic methods. With the advent of biosensors, electrochemical affinity-based biosensors such as those incorporating antibodies and aptamers as biorecognition elements were also reported in the literature. In this review paper, we highlight the success achieved in the design of electrochemical affinity biosensors based on disposable screen-printed electrodes towards detection of protein allergens. We will discuss the analytical figures of merit for various disposable screen-printed affinity sensors in relation to methodologies employed for immobilization of bioreceptors on transducer surface.
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Affiliation(s)
- Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, sector 6, 060101 Bucharest, Romania.
| | - Gilvanda Nunes
- Technological Chemistry Department, Federal University of Maranhão, CCET/UFMA, Av. Portugueses, Cidade Universitária do Canga, 65080-040 São Luis, MA, Brazil.
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM) COMSATS Institute of Information Technology (CIIT), 54000 Lahore, Pakistan.
| | - Usman Latif
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM) COMSATS Institute of Information Technology (CIIT), 54000 Lahore, Pakistan.
| | - Jean-Louis Marty
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France.
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20
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White SP, Sreevatsan S, Frisbie CD, Dorfman KD. Rapid, Selective, Label-Free Aptameric Capture and Detection of Ricin in Potable Liquids Using a Printed Floating Gate Transistor. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00481] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Scott P. White
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Srinand Sreevatsan
- Veterinary
Population Medicine, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - C. Daniel Frisbie
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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21
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Crivianu-Gaita V, Thompson M. Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements. Biosens Bioelectron 2016; 85:32-45. [PMID: 27155114 DOI: 10.1016/j.bios.2016.04.091] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/11/2016] [Accepted: 04/26/2016] [Indexed: 01/14/2023]
Abstract
The choice of biosensing elements is crucial for the development of the optimal biosensor. Three of the most versatile biosensing elements are antibody single-chain Fv fragments (scFv), antibody fragment-antigen binding (Fab') units, and aptamers. This article provides an overview of these three biorecognition elements with respects to their synthesis/engineering, various immobilization techniques, and examples of their use in biosensors. Furthermore, the final section of the review compares and contrasts their characteristics (time/cost of development, ease and variability of immobilization, affinity, stability) illustrating their advantages and disadvantages. Overall, scFv fragments are found to display the highest customizability (i.e. addition of functional groups, immobilizing peptides, etc.) due to recombinant synthesis techniques. If time and cost are an issue in the development of the biosensor, Fab' fragments should be chosen as they are relatively cheap and can be developed quickly from whole antibodies (several days). However, if there are sufficient funds and time is not a factor, aptamers should be utilized as they display the greatest affinity towards their target analytes and are extremely stable (excellent biosensor regenerability).
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Affiliation(s)
| | - Michael Thompson
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
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22
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Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers. J Nucleic Acids 2016; 2016:9718612. [PMID: 27042344 PMCID: PMC4794571 DOI: 10.1155/2016/9718612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/17/2016] [Indexed: 01/10/2023] Open
Abstract
Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface.
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23
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Liu Y, Bhattacharya A, Kuksenok O, He X, Aizenberg M, Aizenberg J, Balazs AC. Computational modeling of oscillating fins that "catch and release" targeted nanoparticles in bilayer flows. SOFT MATTER 2016; 12:1374-1384. [PMID: 26682776 DOI: 10.1039/c5sm02752g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A number of physiological processes in living organisms involve the selective "catch and release" of biomolecules. Inspired by these biological processes, we use computational modeling to design synthetic systems that can controllably catch, transport, and release specific molecules within the surrounding solution, and, thus, could be harnessed for effective separation processes within microfluidic devices. Our system consists of an array of oscillating, microscopic fins that are anchored onto the floor of a microchannel and immersed in a flowing bilayer fluid. The oscillations drive the fins to repeatedly extend into the upper fluid and then tilt into the lower stream. The fins exhibit a specified wetting interaction with the fluids and specific adhesive interactions with nanoparticles in the solution. With this setup, we determine conditions where the oscillating fins can selectively bind, and thus, "catch" target nanoparticles within the upper fluid stream and then release these particles into the lower stream. We isolate the effects of varying the wetting interaction and the fins' oscillation modes on the effective extraction of target species from the upper stream. Our findings provide fundamental insights into the system's complex dynamics and yield guidelines for fabricating devices for the detection and separation of target molecules from complex fluids.
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Affiliation(s)
- Ya Liu
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
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24
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Du Y, Zhen SJ, Li B, Byrom M, Jiang YS, Ellington AD. Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition. Anal Chem 2016; 88:2250-7. [PMID: 26750592 DOI: 10.1021/acs.analchem.5b03930] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, aptasensors have largely been designed on the basis of the notion that ligand-modulated equilibration between aptamer conformations could be exploited for sensing. One implementation of this strategy has been to denature the aptamer with an antisense oligonucleotide, wait for dissociation of the antisense oligonucleotide, and stabilize the folded, signaling conformer with a ligand. However, there is a large kinetic barrier associated with releasing the oligonucleotide from the aptamer to again obtain an active, binding conformation. If the length of the antisense oligonucleotide is decreased to make dissociation from the aptamer more favorable, higher background signals are observed. To improve the general methodology for developing aptasensors, we have developed a novel and robust strategy for aptasensor design in which an oligonucleotide kinetically competes with the ligand for binding rather than having to be released from a stable duplex. While the oligonucleotide can induce conformational change, it initially chooses between the aptamer and a molecular beacon (MB), a process that does not require a lengthy pre-equilibration. Using an anti-ricin aptamer as a starting point, we developed a "competitive" aptasensor with a measured limit of detection (LOD) of 30 nM with an optical readout and as low as 3 nM for ricin toxin A-chain (RTA) detection on an electrochemical platform.
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Affiliation(s)
- Yan Du
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Shu Jun Zhen
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States.,Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , 400715, Chongqing, P.R. China
| | - Bingling Li
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michelle Byrom
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu Sherry Jiang
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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26
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Wang Y, Li H, Xu D. Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection. Anal Chim Acta 2015; 905:149-55. [PMID: 26755149 DOI: 10.1016/j.aca.2015.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/04/2015] [Accepted: 12/12/2015] [Indexed: 12/26/2022]
Abstract
In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China; School of Environmental Science, Nanjing Xiaozhuang University, China.
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
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27
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Vorobyeva M, Timoshenko V, Vorobjev P, Venyaminova A. Aptamers Against Immunologic Targets: Diagnostic and Therapeutic Prospects. Nucleic Acid Ther 2015; 26:52-65. [PMID: 26643948 DOI: 10.1089/nat.2015.0568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The concept of in vitro selection of nucleic acid aptamers emerged 25 years ago, and since then tremendous progress has been achieved in the development of different aptamers and their applications for various bioanalytical and therapeutic purposes. Among other protein targets of aptamers, immune system proteins are of particular interest both as diagnostic markers and therapeutic targets. The present review summarizes up-to-date articles concerning the selection and design of DNA and RNA aptamers against immunologic targets such as antibodies, cytokines, and T-cell and B-cell receptors. We also discuss the prospects of employing aptamers as recognizing modules of diagnostic aptasensors, potential therapeutic candidates for the treatment of autoimmune diseases and cancer, and specific tools for functional studies of immune system proteins.
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Affiliation(s)
- Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentina Timoshenko
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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28
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Nimse SB, Sonawane MD, Song KS, Kim T. Biomarker detection technologies and future directions. Analyst 2015; 141:740-55. [PMID: 26583164 DOI: 10.1039/c5an01790d] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biomarkers play a vital role in disease detection and treatment follow-up. It is important to note that diseases in the early stage are typically treated with the greatest probability of success. However, due to various technical difficulties in current technologies for the detection of biomarkers, the potential of biomarkers is not explored completely. Therefore, the developments of technologies, which can enable the accurate detection of prostate cancer at an early stage with simple, experimental protocols are highly inevitable. This critical review evaluates the current methods and technologies used in the detection of biomarkers. The aim of this article is to provide a comprehensive review covering the advantages and disadvantages of the biomarker detection methods. Future directions for the development of technologies to achieve highly selective and sensitive detection of biomarkers for point-of-care applications are also commented on.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon, 200-702, Korea.
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29
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Hamula CLA, Peng H, Wang Z, Newbigging AM, Tyrrell GJ, Li XF, Le XC. The Effects of SELEX Conditions on the Resultant Aptamer Pools in the Selection of Aptamers Binding to Bacterial Cells. J Mol Evol 2015; 81:194-209. [PMID: 26538121 DOI: 10.1007/s00239-015-9711-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022]
Abstract
Aptamers of high affinity and specificity have a wide range of analytic and clinical applications. Selection of DNA or RNA aptamer molecules usually involves systematic evolution of ligands via exponential enrichment (SELEX), in which a random DNA or RNA library is incubated with a target molecule, and the oligonucleotides that bind the target are then separated from the nonbinders, PCR amplified, and used as refined libraries in the next round of selection. Conventional SELEX methodologies require the use of purified target molecules and their immobilization onto a solid support. However, purified targets from cells are not always available, and fixing the target to a support may alter its conformation. To overcome these problems, we have developed a SELEX technique using live bacterial cells in suspension as targets, for selecting DNA aptamers specific to cell-surface molecules. Through the selection of aptamers binding to Lactobacillus acidophilus and Streptococcus pyogenes, we report here optimization of this technique and show how varying selection conditions impact the characteristics of resultant aptamer pools, including the binding affinity, selectivity, and the secondary structures. We found that the use of larger starting library sequence diversity, gel purification of the subsequent pools, and the introduction of counter-selection resulted in a more efficient SELEX process and more selective aptamers. A SELEX protocol with lower starting sequence diversity, the use of heat denaturation, and the absence of counter-selection still resulted in high-affinity aptamer sequences specific to the target cell types; however, the SELEX process was inefficient, requiring 20 rounds, and the aptamers were not specific to the strain of the bacterial cells. Strikingly, two different SELEX methodologies yielded the same sequence that bound strongly to the target S. pyogenes cells, suggesting the robustness of the bacterial cell-SELEX technique.
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Affiliation(s)
- Camille L A Hamula
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.,Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York City, NY, 10029, USA
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Ashley M Newbigging
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Gregory J Tyrrell
- The Provincial Laboratory for Public Health for Alberta, Walter Mackenzie Health Sciences Centre, Edmonton, AB, T6G 2J2, Canada.,Department of Laboratory Medicine and Pathology, 2B3.08 Walter Mackenzie Health Sciences Centre, University of Alberta, Edmonton, AB, T6G 2B7, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
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30
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Wang Q, Luo B, Yang X, Wang K, Liu L, Du S, Li Z. Elucidation of the effect of aptamer immobilization strategies on the interaction between cell and its aptamer using atomic force spectroscopy. J Mol Recognit 2015; 29:151-8. [PMID: 26530526 DOI: 10.1002/jmr.2514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 09/30/2015] [Indexed: 12/13/2022]
Abstract
The immobilization strategy of cell-specific aptamers is of great importance for studying the interaction between a cell and its aptamer. However, because of the difficulty of studying living cell, there have not been any systematic reports about the effect of immobilization strategies on the binding ability of an immobilized aptamer to its target cell. Because atomic force spectroscopy (AFM) could not only be suitable for the investigation of living cell under physiological conditions but also obtains information reflecting the intrinsic properties of individuals, the effect of immobilization strategies on the interaction of aptamer/human hepatocarcinoma cell Bel-7404 was successively evaluated using AFM here. Two different immobilization methods, including polyethylene glycol immobilization method and glutaraldehyde immobilization method were used, and the factors, such as aptamer orientation, oligodeoxythymidine spacers and dodecyl spacers, were investigated. Binding events measured by AFM showed that a similar unbinding force was obtained regardless of the change of the aptamer orientation, the immobilization method, and spacers, implying that the biophysical characteristics of the aptamer at the molecular level remain undisturbed. However, it showed that the immobilization orientation, immobilization method, and spacers could alter the binding probability of aptamer/Bel-7404 cell. Presumably, these factors may affect the accessibility of the aptamer toward its target cell. These results may provide valuable information for aptamer sensor platforms including ultrasensitive biosensor design.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Bianxia Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Shasha Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
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31
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van den Kieboom CH, van der Beek SL, Mészáros T, Gyurcsányi RE, Ferwerda G, de Jonge MI. Aptasensors for viral diagnostics. Trends Analyt Chem 2015; 74:58-67. [PMID: 32287539 PMCID: PMC7112930 DOI: 10.1016/j.trac.2015.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We discuss progress in aptamer-based detection of viruses. We consider the use of aptasensors for point-of-care diagnostics of viruses. Aptamers have distinct advantages over antibodies for virus recognition. There is strong demand for multiplexed diagnostic measurement of pathogens.
Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.
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Affiliation(s)
- Corné H van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,MTA-BME Research Group for Technical Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
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32
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Cai S, Cao Z, Lau C, Lu J. Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction. Analyst 2015; 139:6022-7. [PMID: 25270599 DOI: 10.1039/c4an01178c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
By using the allosteric hairpin DNA switch, a novel assay for the detection of microRNA (miRNA) let-7a via a hybridization chain reaction (HCR) was introduced. Briefly, the hairpin DNA switch probe is a single-stranded DNA consisting of a streptavidin (SA) aptamer sequence, a target binding sequence and a certain sequence that acts as a trigger of the HCR. In the presence of target let-7a, the hairpin DNA switch would open and expose the stem region sequences, where a part of this sequence acts as initiator sequence strands for the HCR and triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers, another part is the SA aptamer sequence which activates its binding affinity to SA on SA-coated magnetic particles. The hybridization event could be sensitively detected via an instantaneous derivatization reaction between a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotides within the target, the hairpin DNA switch probe, and HCR helices to form an unstable CL intermediate for the generation of light. Our results show that the coupling of the hairpin DNA switch probe and the HCR for the amplified detection of let-7a achieves a better performance (e.g. wide linear response range: 0.1-1000 fmol, low detection limit: 0.1 fmol, and high specificity). Furthermore, this approach could be easily applied to the detection of let-7a in human lung cells, and extended to detect other types of miRNA and proteins such as PDGF based on aptamers. We believe such advancements will represent a significant step towards improved diagnostics and more personalized medical treatment.
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Affiliation(s)
- Sheng Cai
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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33
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Kopra K, Syrjänpää M, Hänninen P, Härmä H. Non-competitive aptamer-based quenching resonance energy transfer assay for homogeneous growth factor quantification. Analyst 2015; 139:2016-23. [PMID: 24611155 DOI: 10.1039/c3an01814h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A non-competitive homogeneous, single-label quenching resonance energy transfer (QRET) assay for protein quantification is now presented using lanthanide-chelate labeled nucleic acid aptamers. A labeled ssDNA aptamer binding to a growth factor has been successfully used to provide luminescence signal protection of the lanthanide label. The QRET technology has previously been applied to competitive assay formats, but now for the first time a direct non-competitive assay is presented. The QRET system is based on the protection of the Eu(iii)-chelate from a soluble quencher molecule when the aptamer interacts with a specific target protein. The direct QRET assay is possible as the aptamer structure itself cannot protect the Eu(iii)-label from quenching. The dynamic range for the optimized vascular endothelial growth factor (VEGF) assay is 0.25-10 nM. A successful quantification of the basic fibroblast growth factor (bFGF) is also demonstrated using the same QRET assay format with a dynamic range of 0.75-50 nM. These assays evidently show the suitability of the direct QRET technique to simple and efficient detection of large biomolecules. The QRET assay can potentially be applied as a detection platform for any other protein targets with a known aptamer sequence.
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Affiliation(s)
- Kari Kopra
- Laboratory of Biophysics, Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Tykistökatu 6 A 5th floor, FI-20520 Turku, Finland.
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Pilehvar S, Jambrec D, Gebala M, Schuhmann W, De Wael K. Intercalation of Proflavine in ssDNA Aptamers: Effect on Binding of the Specific Target Chloramphenicol. ELECTROANAL 2015. [DOI: 10.1002/elan.201500192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Martin JA, Mirau PA, Chushak Y, Chávez JL, Naik RR, Hagen JA, Kelley-Loughnane N. Single-Round Patterned DNA Library Microarray Aptamer Lead Identification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:137489. [PMID: 26075138 PMCID: PMC4446497 DOI: 10.1155/2015/137489] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface.
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Affiliation(s)
- Jennifer A. Martin
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Peter A. Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Yaroslav Chushak
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Jorge L. Chávez
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- UES Inc., 4401 Dayton-Xenia Road, Dayton, Dayton, OH 45433, USA
| | - Rajesh R. Naik
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Joshua A. Hagen
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Nancy Kelley-Loughnane
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
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Kobayashi R, Biyani M, Ueno S, Kumal SR, Kuramochi H, Ichiki T. Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules. Biosens Bioelectron 2015; 67:115-20. [DOI: 10.1016/j.bios.2014.07.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/19/2014] [Accepted: 07/22/2014] [Indexed: 11/30/2022]
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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Shastri A, McGregor LM, Liu Y, Harris V, Nan H, Mujica M, Vasquez Y, Bhattacharya A, Ma Y, Aizenberg M, Kuksenok O, Balazs AC, Aizenberg J, He X. An aptamer-functionalized chemomechanically modulated biomolecule catch-and-release system. Nat Chem 2015; 7:447-54. [PMID: 25901824 DOI: 10.1038/nchem.2203] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/12/2015] [Indexed: 12/23/2022]
Abstract
The efficient extraction of (bio)molecules from fluid mixtures is vital for applications ranging from target characterization in (bio)chemistry to environmental analysis and biomedical diagnostics. Inspired by biological processes that seamlessly synchronize the capture, transport and release of biomolecules, we designed a robust chemomechanical sorting system capable of the concerted catch and release of target biomolecules from a solution mixture. The hybrid system is composed of target-specific, reversible binding sites attached to microscopic fins embedded in a responsive hydrogel that moves the cargo between two chemically distinct environments. To demonstrate the utility of the system, we focus on the effective separation of thrombin by synchronizing the pH-dependent binding strength of a thrombin-specific aptamer with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, and show a non-destructive separation that has a quantitative sorting efficiency, as well as the system's stability and amenability to multiple solution recycling.
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Affiliation(s)
- Ankita Shastri
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lynn M McGregor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ya Liu
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Valerie Harris
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Hanqing Nan
- Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Maritza Mujica
- Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Yolanda Vasquez
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amitabh Bhattacharya
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Yongting Ma
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Michael Aizenberg
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Olga Kuksenok
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Anna C Balazs
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Joanna Aizenberg
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA [3] Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA [4] Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ximin He
- 1] Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA [2] Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA [3] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
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Chen L, Sha L, Qiu Y, Wang G, Jiang H, Zhang X. An amplified electrochemical aptasensor based on hybridization chain reactions and catalysis of silver nanoclusters. NANOSCALE 2015; 7:3300-8. [PMID: 25623467 DOI: 10.1039/c4nr06664b] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the present study, based on the mimic oxidase catalytic character of nucleic-acid-stabilized silver nanoclusters (DNA/AgNCs) and hybridization chain reactions for signal amplification, the fabrication of a label-free sensitive "turn-on" electrochemical aptasensor for the amplified determination of lysozyme was demonstrated. First, the designed DNA duplex was modified on the electrode. With the specific binding of the target, lysozyme and its aptamer, the lysozyme-binding DNA sequence was liberated, exposing the induced DNA sequence, which in turn triggered the formation of the supersandwich DNA structure. Because the cytosine-rich sequence was designed ingeniously on the DNA sequence, DNA/AgNCs were formed on the supersandwich DNA structure. The peroxidase-like character of DNA/AgNCs produced detectable electrochemical signals for the lysozyme aptasensor, which showed a satisfying sensitive detection of lysozyme with a low detection limit of 42 pM and a wide linear range of 10(-10) M to 10(-5) M.
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Affiliation(s)
- Ling Chen
- Key Laboratory of Chem-Biosensing, Anhui province; Key Laboratory of Functional Molecular Solids, Anhui province; College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Normal University, Wuhu 241000, PR China.
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40
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Saberian-Borujeni M, Johari-Ahar M, Hamzeiy H, Barar J, Omidi Y. Nanoscaled aptasensors for multi-analyte sensing. ACTA ACUST UNITED AC 2014; 4:205-15. [PMID: 25671177 PMCID: PMC4298712 DOI: 10.15171/bi.2014.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/03/2014] [Accepted: 11/08/2014] [Indexed: 12/21/2022]
Abstract
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Introduction: Nanoscaled aptamers (Aps), as short single-stranded DNA or RNA oligonucleotides, are able to bind to their specific targets with high affinity, upon which they are considered as powerful diagnostic and analytical sensing tools (the so-called "aptasensors"). Aptamers are selected from a random pool of oligonucleotides through a procedure known as "systematic evolution of ligands by exponential enrichment".
Methods: In this work, the most recent studies in the field of aptasensors are reviewed and discussed with a main focus on the potential of aptasensors for the multianalyte detection(s).
Results: Due to the specific folding capability of aptamers in the presence of analyte, aptasensors have substantially successfully been exploited for the detection of a wide range of small and large molecules (e.g., drugs and their metabolites, toxins, and associated biomarkers in various diseases) at very low concentrations in the biological fluids/samples even in presence of interfering species.
Conclusion: Biological samples are generally considered as complexes in the real biological media. Hence, the development of aptasensors with capability to determine various targets simultaneously within a biological matrix seems to be our main challenge. To this end, integration of various key scientific dominions such as bioengineering and systems biology with biomedical researches are inevitable.
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Affiliation(s)
- Mehdi Saberian-Borujeni
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Johari-Ahar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Hamzeiy
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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42
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Kim E, Paeng IR. Advantageous sensitivity in the DNA homolog of the RNA dopamine aptamer. J Immunoassay Immunochem 2014; 35:83-100. [PMID: 24063619 DOI: 10.1080/15321819.2013.792833] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A competitive enzyme-linked aptamer assay for DA was performed by using two aptamers, individually; one is a 57 mer-RNA aptamer and the other is its homolog DNA aptamer. The difference between the RNA aptamer and the DNA aptamer are based on their particular nucleotides. It is known that the lack of a hydroxyl group in the 2' position of DNA is related with its chemical and biological stability. Thus, the use of the DNA homolog of the RNA aptamer could improve the affinity toward DA due to stability and finally, lower the detection limit. In this paper, we report advantageous sensitivity and specificity of its homolog DNA aptamer assay as compared to the RNA aptamer assay. Both aptamer assays were performed with 0.01 µg mL⁻¹ of each aptamer and 1.205 × 10⁻⁸ M DA-HRP conjugate using the optimized method. A dose-response curve was constructed, and the limit of detection for the DA was determined as 6.3 × 10⁻⁸ M for RNA aptamer assay, and 3.2 × 10⁻¹² M for the homolog DNA aptamer assay, respectively. These results demonstrated that the assay sensitivity was more than 10⁴ times improved with the DNA homolog of the RNA aptamer compared to its original RNA aptamer obtained through SELEX process. Also these results confirmed that the DNA homolog of the RNA aptamer can maintained the binding site and retained a function in both structure. Thus, the switching to the DNA version of RNA aptamer is possible to bind more stably and still able to bind to dopamine.
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Affiliation(s)
- Eunhye Kim
- a Department of Chemistry , Seoul Women's University , Seoul , Republic of Korea
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43
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Guarrotxena N, Bazan GC. Antitags: SERS-encoded nanoparticle assemblies that enable single-spot multiplex protein detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1941-1946. [PMID: 24338905 DOI: 10.1002/adma.201304107] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/04/2013] [Indexed: 06/03/2023]
Abstract
Simultaneous detection of multiple proteins on a single spot can be efficiently achieved by using multiplexed surface-enhanced Raman spectroscopy (SERS)-encoded nanoparticle 'antitags' consisting of poly(ethylene glycol) (PEG)-protected silver dimers (and higher aggregates) and antibody-tagging entities. The effective SERS-based multivariate deconvolution approach guarantees an accurate and successful distinguishable identification of single and multiple proteins in complex samples. Their potential application in multiplexed SERS bioimaging technology can be easily envisaged.
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Affiliation(s)
- Nekane Guarrotxena
- Instituto de Ciencia y Tecnología de Polímeros (ICTP), Consejo Superior de Investigaciones Científicas (CSIC), Juan de la Cierva 3, Madrid, 28006, Spain
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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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45
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Szkola A, Linares EM, Worbs S, Dorner BG, Dietrich R, Märtlbauer E, Niessner R, Seidel M. Rapid and simultaneous detection of ricin, staphylococcal enterotoxin B and saxitoxin by chemiluminescence-based microarray immunoassay. Analyst 2014; 139:5885-92. [DOI: 10.1039/c4an00345d] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Simultaneous detection of proteotoxins, ricin and SEB, and small toxin, STX, on a chemiluminescence-based microarray using anti-idiotypic antibody for STX.
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Affiliation(s)
- A. Szkola
- Chair for Analytical Chemistry & Institute of Hydrochemistry
- TU München
- 81377 Munich, Germany
| | - E. M. Linares
- Chair for Analytical Chemistry & Institute of Hydrochemistry
- TU München
- 81377 Munich, Germany
| | - S. Worbs
- Centre for Biological Threats and Special Pathogens
- Biological Toxins
- Robert Koch-Institut
- 13353 Berlin, Germany
| | - B. G. Dorner
- Centre for Biological Threats and Special Pathogens
- Biological Toxins
- Robert Koch-Institut
- 13353 Berlin, Germany
| | - R. Dietrich
- Chair of Hygiene and Technology of Milk
- LMU München
- 85764 Oberschleißheim, Germany
| | - E. Märtlbauer
- Chair of Hygiene and Technology of Milk
- LMU München
- 85764 Oberschleißheim, Germany
| | - R. Niessner
- Chair for Analytical Chemistry & Institute of Hydrochemistry
- TU München
- 81377 Munich, Germany
| | - M. Seidel
- Chair for Analytical Chemistry & Institute of Hydrochemistry
- TU München
- 81377 Munich, Germany
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Römhildt L, Pahlke C, Zörgiebel F, Braun HG, Opitz J, Baraban L, Cuniberti G. Patterned biochemical functionalization improves aptamer-based detection of unlabeled thrombin in a sandwich assay. ACS APPLIED MATERIALS & INTERFACES 2013; 5:12029-35. [PMID: 24171544 DOI: 10.1021/am4038245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Here we propose a platform for the detection of unlabeled human α-thrombin down to the picomolar range in a fluorescence-based aptamer assay. In this concept, thrombin is captured between two different thrombin binding aptamers, TBA1 (15mer) and TBA2 (29mer), each labeled with a specific fluorescent dye. One aptamer is attached to the surface, the second one is in solution and recognizes surface-captured thrombin. To improve the limit of detection and the comparability of measurements, we employed and compared two approaches to pattern the chip substrate-microcontact printing of organosilanes onto bare glass slides, and controlled printing of the capture aptamer TBA1 in arrays onto functionalized glass substrates using a nanoplotter device. The parallel presence of functionalized and control areas acts as an internal reference. We demonstrate that both techniques enable the detection of thrombin concentrations in a wide range from 0.02 to 200 nM with a detection limit at 20 pM. Finally, the developed method could be transferred to any substrate to probe different targets that have two distinct possible receptors without the need for direct target labeling.
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Affiliation(s)
- Lotta Römhildt
- Institute for Materials Science and Max Bergmann Center of Biomaterials and §Center for Advancing Electronics Dresden, TU Dresden , 01062 Dresden, Germany
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Xie L, Yan X, Du Y. An aptamer based wall-less LSPR array chip for label-free and high throughput detection of biomolecules. Biosens Bioelectron 2013; 53:58-64. [PMID: 24121209 DOI: 10.1016/j.bios.2013.09.031] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 12/14/2022]
Abstract
Despite recent progress in localized surface plasmon resonance (LSPR) based bio-sensing, it remains challenging to achieve sensitive and high throughput LSPR detection with facilities available in common laboratories. Here we developed a wall-less LSPR array chip for facile, label-free and high throughput detection of biomolecules using a normal microplate reader. The wall-less LSPR array chip was fabricated by immobilizing plasmonic nanoparticles (NPs) on a hydrophilic-hydrophobic patterned glass slide, enabling high throughput detection. The wall-less configuration simplifies chip fabrication and sample processing, and enables miniaturization to significantly reduce sample and reagent consumption. A double-gold NPs enhanced system comprising of 13-nm-gold NPs conjugated to aptamer modified 39-nm-gold NPs on glass substrate was adopted to constitute competitive replacement assay for signal amplification in small molecule (i.e. ATP) detection. Upon enhancement, the detection sensitivity of ATP was augmented by 5 orders of magnitude from 0.01 µM to 100 µM measured by the laboratory microplate reader. The wall-less LSPR sensor chip can be widely applied for miniaturized and high throughput detection of a variety of targets in biomedical applications and environmental monitoring using facilities available in common laboratories.
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Affiliation(s)
- Liping Xie
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Franssen-van Hal NLW, van der Putte P, Hellmuth K, Matysiak S, Kretschy N, Somoza MM. Optimized light-directed synthesis of aptamer microarrays. Anal Chem 2013; 85:5950-7. [PMID: 23672295 PMCID: PMC3686109 DOI: 10.1021/ac400746j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Aptamer microarrays are a promising
high-throughput method for
ultrasensitive detection of multiple analytes, but although much is
known about the optimal synthesis of oligonucleotide microarrays used
in hybridization-based genomics applications, the bioaffinity interactions
between aptamers and their targets is qualitatively different and
requires significant changes to synthesis parameters. Focusing on
streptavidin-binding DNA aptamers, we employed light-directed in situ
synthesis of microarrays to analyze the effects of sequence fidelity,
linker length, surface probe density, and substrate functionalization
on detection sensitivity. Direct comparison with oligonucleotide hybridization
experiments indicates that aptamer microarrays are significantly more
sensitive to sequence fidelity and substrate functionalization and
have different optimal linker length and surface probe density requirements.
Whereas microarray hybridization probes generate maximum signal with
multiple deletions, aptamer sequences with the same deletion rate
result in a 3-fold binding signal reduction compared with the same
sequences synthesized for maximized sequence fidelity. The highest
hybridization signal was obtained with dT 5mer linkers, and the highest
aptamer signal was obtained with dT 11mers, with shorter aptamer linkers
significantly reducing the binding signal. The probe hybridization
signal was found to be more sensitive to molecular crowding, whereas
the aptamer probe signal does not appear to be constrained within
the density of functional surface groups commonly used to synthesize
microarrays.
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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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50
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Nimse SB, Song KS, Kim J, Sayyed DR, Kim T. 9G DNAChip Technology: Self-Assembled Monolayer (SAM) of ssDNA for Ultra-Sensitive Detection of Biomarkers. Int J Mol Sci 2013; 14:5723-33. [PMID: 23481635 PMCID: PMC3634481 DOI: 10.3390/ijms14035723] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/01/2013] [Accepted: 03/04/2013] [Indexed: 11/16/2022] Open
Abstract
A 9G DNAChip obtained by allowing the formation of a self-assembled monolayer (SAM) of oligonucleotides appended with nine consecutive guanines on the chip surface has been applied in the detection of biomarkers. Using a 9G DNAChip, biomarker in the concentration range of 4 pg/mL to 40 fg/mL can be easily differentiated in the buffer matrix. Moreover, it is the first time that a biomarker with a concentration of 40 fg/mL has been detected in a mixture of proteins without use of any signal amplification technique.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
| | - Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; E-Mails: (K.-S.S.); (J.K.)
| | - Junghoon Kim
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; E-Mails: (K.-S.S.); (J.K.)
| | - Danishmalik Rafiq Sayyed
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-33-248-2078 (ext. 123); Fax: +82-33-256-3421
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