51
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Renuka RM, Achuth J, Chandan HR, Venkataramana M, Kadirvelu K. A fluorescent dual aptasensor for the rapid and sensitive onsite detection ofE. coliO157:H7 and its validation in various food matrices. NEW J CHEM 2018. [DOI: 10.1039/c8nj00997j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The speedy analysis of food products remains a keen area of concern; thus, rapid, highly efficient and robust on-site detection platforms are essential.
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Affiliation(s)
- R. M. Renuka
- Molecular Immunology Laboratory
- DRDO-BU-CLS
- Coimbatore-641046
- India
| | - J. Achuth
- Molecular Immunology Laboratory
- DRDO-BU-CLS
- Coimbatore-641046
- India
| | - H. R. Chandan
- Center for Nano and Material Sciences
- Jain University
- Bangalore
- India
| | - M. Venkataramana
- Molecular Immunology Laboratory
- DRDO-BU-CLS
- Coimbatore-641046
- India
| | - K. Kadirvelu
- Molecular Immunology Laboratory
- DRDO-BU-CLS
- Coimbatore-641046
- India
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52
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Ausländer S, Fussenegger M. Synthetic RNA-based switches for mammalian gene expression control. Curr Opin Biotechnol 2017; 48:54-60. [DOI: 10.1016/j.copbio.2017.03.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/10/2017] [Indexed: 01/25/2023]
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53
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QIN SY, CHEN ND, WANG Q, HUANG J, HE XX, LIU JB, GUO QP, YANG XH, WANG KM. Application of Nucleic Acid Aptamers in Polypeptides Researches. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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54
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Lee KH, Zeng H. Aptamer-Based ELISA Assay for Highly Specific and Sensitive Detection of Zika NS1 Protein. Anal Chem 2017; 89:12743-12748. [PMID: 29120623 DOI: 10.1021/acs.analchem.7b02862] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report here a few Zika NS1-binding ssDNA aptamers selected using the conventional SELEX protocol, and their application in an ELISA assay for sensitive diagnosis of Zika NS1 protein. Among the aptamers identified, aptamers 2 and 10 could recognize different binding epitopes of Zika NS1 protein. This complementary in binding site, when coupled with an extraordinarily high binding affinity by 2 (41-nt, KD = 45 pM) and high specificity by 10, was used successfully to construct an ELISA-based assay where 2 and 10 serve as the capture and detection agents, respectively, giving rise to a highly specific detection of Zika NS1 with a detection limit of 100 ng/mL in buffer. Further testing of a few in-house anti-Zika NS1 antibodies show that 2 could also pair with an anti-Zika NS1 antibody. Such aptamer-antibody pairing not only lowers the detection sensitivity by 3 orders of magnitude to 0.1 ng/mL in buffer but also enable highly sensitive detection of as low as 1 and 10 ng/mL of Zika NS1 to be carried out in 10% and 100% human serum, respectively. These results suggest that the selected aptamers would be useful for medical diagnosis of Zika virus infection in various aptamer-based diagnostic devices including ELISA assay.
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Affiliation(s)
- Kyung Hyun Lee
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, Singapore 138669
| | - Huaqiang Zeng
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, Singapore 138669
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55
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Fülle L, Steiner N, Funke M, Gondorf F, Pfeiffer F, Siegl J, Opitz FV, Haßel SK, Erazo AB, Schanz O, Stunden HJ, Blank M, Gröber C, Händler K, Beyer M, Weighardt H, Latz E, Schultze JL, Mayer G, Förster I. RNA Aptamers Recognizing Murine CCL17 Inhibit T Cell Chemotaxis and Reduce Contact Hypersensitivity In Vivo. Mol Ther 2017; 26:95-104. [PMID: 29103909 PMCID: PMC5763148 DOI: 10.1016/j.ymthe.2017.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023] Open
Abstract
The chemokine CCL17, mainly produced by dendritic cells (DCs) in the immune system, is involved in the pathogenesis of various inflammatory diseases. As a ligand of CCR4, CCL17 induces chemotaxis and facilitates T cell-DC interactions. We report the identification of two novel RNA aptamers, which were validated in vitro and in vivo for their capability to neutralize CCL17. Both aptamers efficiently inhibited the directed migration of the CCR4+ lymphoma line BW5147.3 toward CCL17 in a dose-dependent manner. To study the effect of these aptamers in vivo, we used a murine model of contact hypersensitivity. Systemic application of the aptamers significantly prevented ear swelling and T cell infiltration into the ears of sensitized mice after challenge with the contact sensitizer. The results of this proof-of-principle study establish aptamers as potent inhibitors of CCL17-mediated chemotaxis. Potentially, CCL17-specific aptamers may be used therapeutically in humans to treat or prevent allergic and inflammatory diseases.
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Affiliation(s)
- Lorenz Fülle
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Nancy Steiner
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Markus Funke
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Fabian Gondorf
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Franziska Pfeiffer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julia Siegl
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Friederike V Opitz
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Silvana K Haßel
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Anna Belen Erazo
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Oliver Schanz
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - H James Stunden
- Institute of Innate Immunity, University Hospital Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Michael Blank
- AptaIT, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany
| | - Carsten Gröber
- AptaIT, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany; Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Heike Weighardt
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn, Sigmund-Freud-Straße 27, 53127 Bonn, Germany
| | - Günter Mayer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Centre of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Irmgard Förster
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany.
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56
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Agyei D, Acquah C, Tan KX, Hii HK, Rajendran SRCK, Udenigwe CC, Danquah MK. Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food. Anal Bioanal Chem 2017; 410:297-306. [PMID: 28884330 DOI: 10.1007/s00216-017-0599-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/01/2017] [Accepted: 08/22/2017] [Indexed: 12/28/2022]
Abstract
Food-derived bioactive proteins and peptides have gained acceptance among researchers, food manufacturers and consumers as health-enhancing functional food components that also serve as natural alternatives for disease prevention and/or management. Bioactivity in food proteins and peptides is determined by their conformations and binding characteristics, which in turn depend on their primary and secondary structures. To maintain their bioactivities, the molecular integrity of bioactive peptides must remain intact, and this warrants the study of peptide form and structure, ideally with robust, highly specific and sensitive techniques. Short single-stranded nucleic acids (i.e. aptamers) are known to have high affinity for cognate targets such as proteins and peptides. Aptamers can be produced cost-effectively and chemically derivatized to increase their stability and shelf life. Their improved binding characteristics and minimal modification of the target molecular signature suggests their suitability for real-time detection of conformational changes in both proteins and peptides. This review discusses the developmental progress of systematic evolution of ligands by exponential enrichment (SELEX), an iterative technology for generating cost-effective aptamers with low dissociation constants (K d) for monitoring the form and structure of bioactive proteins and peptides. The review also presents case studies of this technique in monitoring the structural stability of bioactive peptide formulations to encourage applications in functional foods. The challenges and potential of aptamers in this research field are also discussed. Graphical abstract Advancing bioactive proteins and peptide functionality via aptameric ligands.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Kei Xian Tan
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Hieng Kok Hii
- Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Subin R C K Rajendran
- Verschuren Centre for Sustainability in Energy and the Environment, Cape Breton University, Sydney, NS, B1P 6L2, Canada
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Michael K Danquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia. .,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia.
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57
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Malekzad H, Zangabad PS, Mirshekari H, Karimi M, Hamblin MR. Noble metal nanoparticles in biosensors: recent studies and applications. NANOTECHNOLOGY REVIEWS 2017; 6:301-329. [PMID: 29335674 PMCID: PMC5766271 DOI: 10.1515/ntrev-2016-0014] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers and receptor immobilization, good ability for reaction catalysis and electron transfer, and good biocompatibility. MNPs can be used alone and in combination with other classes of nanostructures. MNP-based sensors can lead to significant signal amplification, higher sensitivity, and great improvements in the detection and quantification of biomolecules and different ions. Some recent examples of biomolecular sensors using MNPs are given, and the effects of structure, shape, and other physical properties of noble MNPs and nanohybrids in biosensor performance are discussed.
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Affiliation(s)
- Hedieh Malekzad
- Faculty of Chemistry, Kharazmi University, South Mofatteh Ave, P.O. Box 15719-14911, Tehran, Iran; and Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
| | - Parham Sahandi Zangabad
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Science (TUOMS), Tabriz, Iran; Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran; and Department of Materials Science and Engineering, Sharif University of Technology, P.O. Box 11365-9466, 14588 Tehran, Iran
| | - Hamed Mirshekari
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
| | - Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Hemmat Exp. Way, P.O. Box 14665-354, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; and Division of Health Sciences and Technology, Harvard-MIT, Cambridge, MA 02139, USA
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58
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Lee KH, Zeng H. A general double library SELEX strategy for aptamer selection using unmodified nonimmobilized targets. Anal Bioanal Chem 2017. [DOI: 10.1007/s00216-017-0454-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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59
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Maio G, Enweronye O, Zumrut HE, Batool S, Van N, Mallikaratchy P. Systematic optimization and modification of a DNA aptamer with 2'-O-methyl RNA analogues. ChemistrySelect 2017; 2:2335-2340. [PMID: 29226219 DOI: 10.1002/slct.201700359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nucleic acid aptamers (NAAs) are short synthetic DNA or RNA molecules that specifically fold into distinct three-dimensional structures able to specifically recognize a target. While NAAs show unprecedented promise in a variety of applications, including sensing, therapeutics and diagnostics, one major limitation involves the lack of stability towards omnipresent nucleases. Therefore, we herein report a systematic truncation and incorporation of 2'-O-methyl bases to a DNA aptamer, which results in increased stability without affecting affinity. One of the newly designed analogues is stable up to 24 hours, demonstrating that 2'-O-methyl RNA is an attractive modification to DNA aptamers, especially when therapeutic applications are intended.
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Affiliation(s)
- George Maio
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Osita Enweronye
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Hasan E Zumrut
- Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sana Batool
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Nabeela Van
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468.,Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.,Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
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60
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Qin S, Chen N, Yang X, Wang Q, Wang K, Huang J, Liu J, Zhou M. Development of Dual-Aptamers for Constructing Sandwich-Type Pancreatic Polypeptide Assay. ACS Sens 2017; 2:308-315. [PMID: 28723135 DOI: 10.1021/acssensors.6b00836] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pancreatic polypeptide (PP) is a specific biomarker of nonfunctional pancreatic neuroendocrine tumors (NF-pNETs). Clinical significance of PP inspires researchers to make great efforts in developing sensitive and specific sensors. However, there is no existing biosensor for detecting PP that combines facility and functionality. Addressing this challenge, a pair of aptamers which could be used to develop a sandwich assay for PP is reported. First, several high affinity aptamers are screened through graphene oxide-based SELEX, and appropriate dual-aptamers which could bind to different epitopes of PP are identified through fluorescence assays. Then the feasibility of the dual-aptamers for constructing the sandwich assay is validated via dynamic light scattering. This sandwich assay shows considerable sensitivity and specificity. The above results imply that the dual-aptamers have the potential toward developing novel sensors for PP in clinical samples.
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Affiliation(s)
- Shiya Qin
- 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
| | - Nandi Chen
- 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
| | - 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
| | - 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
| | - Jin Huang
- 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
| | - Jianbo 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
| | - Maogui Zhou
- 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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61
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Percze K, Szakács Z, Scholz É, András J, Szeitner Z, Kieboom CHVD, Ferwerda G, Jonge MID, Gyurcsányi RE, Mészáros T. Aptamers for respiratory syncytial virus detection. Sci Rep 2017; 7:42794. [PMID: 28220811 PMCID: PMC5318870 DOI: 10.1038/srep42794] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/17/2017] [Indexed: 01/04/2023] Open
Abstract
The identification of the infectious agents is pivotal for appropriate care of patients with viral diseases. Current viral diagnostics rely on selective detection of viral nucleic acid or protein components. In general, detection of proteins rather than nucleic acids is technically more suitable for rapid tests. However, protein-based virus identification methods depend on antibodies limiting the practical applicability of these approaches. Aptamers rival antibodies in target selectivity and binding affinity, and excel in terms of robustness and cost of synthesis. Although aptamers have been generated for virus identification in laboratory settings, their introduction into routine virus diagnostics has not been realized, yet. Here, we demonstrate that the rationally designed SELEX protocol can be applied on whole virus to select aptamers, which can potentially be applied for viral diagnostics. This approach does not require purified virus protein or complicated virus purification. The presented data also illustrate that corroborating the functionality of aptamers with various approaches is essential to pinpoint the most appropriate aptamer amongst the panel of candidates obtained by the selection. Our protocol yielded aptamers capable of detecting respiratory syncytial virus (RSV), an important pathogen causing severe disease especially in young infants, at clinically relevant concentrations in complex matrices.
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Affiliation(s)
- Krisztina Percze
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zoltán Szakács
- MTA-BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111, Budapest, Hungary
| | - Éva Scholz
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Judit András
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Szeitner
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Corné H. van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marien I. de Jonge
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Róbert E. Gyurcsányi
- MTA-BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, 1111, Budapest, Hungary
| | - 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
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62
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Haddache F, Le Goff A, Spinelli N, Gairola P, Gorgy K, Gondran C, Defrancq E, Cosnier S. A label-free photoelectrochemical cocaine aptasensor based on an electropolymerized ruthenium-intercalator complex. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.09.127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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63
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High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency. Sci Rep 2016; 6:33697. [PMID: 27652575 PMCID: PMC5031971 DOI: 10.1038/srep33697] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/31/2016] [Indexed: 12/25/2022] Open
Abstract
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.
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64
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Kazane I, Gorgy K, Gondran C, Spinelli N, Zazoua A, Defrancq E, Cosnier S. Highly Sensitive Bisphenol-A Electrochemical Aptasensor Based on Poly(Pyrrole-Nitrilotriacetic Acid)-Aptamer Film. Anal Chem 2016; 88:7268-73. [DOI: 10.1021/acs.analchem.6b01574] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Imen Kazane
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
- Université de Jijel, Laboratoire de Matériaux:
Elaborations-Propriétés-Applications, BP 98, Ouled Aissa, 18000 Jijel, Algeria
| | - Karine Gorgy
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
| | - Chantal Gondran
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
| | - Nicolas Spinelli
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
| | - Ali Zazoua
- Université de Jijel, Laboratoire de Matériaux:
Elaborations-Propriétés-Applications, BP 98, Ouled Aissa, 18000 Jijel, Algeria
| | - E. Defrancq
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
| | - Serge Cosnier
- Univ.
Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, 570 rue de la Chimie, CS 40700, 38058 Grenoble cedex 9, France
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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Valenzano S, De Girolamo A, DeRosa MC, McKeague M, Schena R, Catucci L, Pascale M. Screening and Identification of DNA Aptamers to Tyramine Using in Vitro Selection and High-Throughput Sequencing. ACS COMBINATORIAL SCIENCE 2016; 18:302-13. [PMID: 27057927 DOI: 10.1021/acscombsci.5b00163] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aptamers are synthetic single-stranded DNA or RNA sequences that can fold into tertiary structures allowing them to interact with and bind to targets with high affinity and specificity. This paper describes the first selection and identification of DNA aptamers able to recognize the biogenic amine tyramine. To successfully isolate aptamers to this challenging small molecule target, the SELEX methodology was adapted by combining a systematic strategy to increase the selection stringency and monitor enrichment success. As the benefits of applying high-throughput sequencing (HTS) in SELEX experiments is becoming more clear, this method was employed in combination with bioinformatics analysis to evaluate the utility of the selection strategy and to uncover new potential high affinity sequences. On the basis of the presence of consensus regions (sequence families) and family similarities (clusters), 15 putative aptamers to tyramine were identified. A recently described workflow approach to perform a primary screening and characterization of the aptamer candidates by microequilibrium dialysis and by microscale thermophoresis was next leveraged. These candidate aptamers exhibited dissociation constant (Kd) values in the range of 0.2-152 μM with aptamer Tyr_10 as the most promising one followed by aptamer Tyr_14. These aptamers could be used as promising molecular recognition tools for the development of inexpensive, robust and innovative biosensor platforms for the detection of tyramine in food and beverages.
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Affiliation(s)
- Stefania Valenzano
- Institute
of Sciences of Food Production, National Research Council of Italy, via G. Amendola 122/O, 70126 Bari, Italy
| | - Annalisa De Girolamo
- Institute
of Sciences of Food Production, National Research Council of Italy, via G. Amendola 122/O, 70126 Bari, Italy
| | - Maria C. DeRosa
- Chemistry
Department, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario Canada K1S 5B6
| | - Maureen McKeague
- Chemistry
Department, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario Canada K1S 5B6
| | - Roberto Schena
- Institute
of Sciences of Food Production, National Research Council of Italy, via G. Amendola 122/O, 70126 Bari, Italy
| | - Lucia Catucci
- Chemistry
Department, University of Bari “Aldo Moro”, via Orabona
4, 70126 Bari, Italy
| | - Michelangelo Pascale
- Institute
of Sciences of Food Production, National Research Council of Italy, via G. Amendola 122/O, 70126 Bari, Italy
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67
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Wei B, Zhang J, Wang H, Xia F. A new electrochemical aptasensor based on a dual-signaling strategy and supersandwich assay. Analyst 2016; 141:4313-8. [PMID: 27188283 DOI: 10.1039/c6an00594b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this study, we develop a new electrochemical aptasensor by coupling two amplification strategies, including a dual signaling strategy and a supersandwich assay. In order to fabricate this aptasensor, a thiolated capture probe (CP) was first self-assembled on the gold electrode surface by Au-S bonds. After the addition of methylene blue (MB) modified signal probe 1 (SP1) and ferrocene (Fc) labeled signal probe 2 (SP2), supersandwich structure DNA, including multiple units of SP1 and SP2, was grown from the CP on the electrode surface. In the presence of ATP, the strong interaction between ATP and its aptamer (CP, SP1) leads to the disassembly of the supersandwich structure and thereby, the release of SP1 and SP2 from the gold electrode surface, resulting in a decrease of the MB and Fc signals. Taking "Signal gainMB + Signal gainFc" as the response signal, ATP can be detected sensitively; the detection limit is 2.1 nM, which is lower than that using either a single-signaling strategy or a traditional sandwich assay alone. Moreover, the new aptasensor also exhibits excellent specificity, selectivity, reliability and applicability. We believe that this new strategy will be helpful for fabricating sensitive and selective electrochemical aptasensors of other biomolecules and small molecules.
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Affiliation(s)
- Benmei Wei
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, P. R. China.
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68
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Miranda-Castro R, de-los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Harnessing Aptamers to Overcome Challenges in Gluten Detection. BIOSENSORS-BASEL 2016; 6:16. [PMID: 27104578 PMCID: PMC4931476 DOI: 10.3390/bios6020016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 12/13/2022]
Abstract
Celiac disease is a lifelong autoimmune disorder triggered by foods containing gluten, the storage protein in wheat, rye, and barley. The rapidly escalating number of patients diagnosed with this disease poses a great challenge to both food industry and authorities to guarantee food safety for all. Therefore, intensive efforts are being made to establish minimal disease-eliciting doses of gluten and consequently to improve gluten-free labeling. These efforts depend to a high degree on the availability of methods capable of detecting the protein in food samples at levels as low as possible. Current analytical approaches rely on the use of antibodies as selective recognition elements. With limited sensitivity, these methods exhibit some deficiencies that compromise the accuracy of the obtained results. Aptamers provide an ideal alternative for designing biosensors for fast and selective measurement of gluten in foods. This article highlights the challenges in gluten detection, the current status of the use of aptamers for solving this problem, and what remains to be done to move these systems into commercial applications.
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Affiliation(s)
- Rebeca Miranda-Castro
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
| | | | - Arturo J Miranda-Ordieres
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
| | - María Jesús Lobo-Castañón
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
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69
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Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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70
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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71
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Dirkzwager RM, Liang S, Tanner JA. Development of Aptamer-Based Point-of-Care Diagnostic Devices for Malaria Using Three-Dimensional Printing Rapid Prototyping. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00175] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Roderick M. Dirkzwager
- School of Biomedical Sciences,
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S. A. R. China
| | - Shaolin Liang
- School of Biomedical Sciences,
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S. A. R. China
| | - Julian A. Tanner
- School of Biomedical Sciences,
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S. A. R. China
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72
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Gu H, Duan N, Wu S, Hao L, Xia Y, Ma X, Wang Z. Graphene oxide-assisted non-immobilized SELEX of okdaic acid aptamer and the analytical application of aptasensor. Sci Rep 2016; 6:21665. [PMID: 26898784 PMCID: PMC4761938 DOI: 10.1038/srep21665] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Okadaic acid (OA) is a low-molecular-weight marine toxin from shellfish that causes abdominal pain, vomiting and diarrhea, i.e., diarrheic shellfish poisoning. In this study, a ssDNA aptamer that specifically binds to OA with high affinity was obtained via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assisted by graphene oxide (GO). This aptamer was then applied to fabricate a novel direct competitive enzyme-linked aptamer assay (ELAA). At the optimized conditions, this ELAA method showed a low detection limit (LOD of 0.01 ng/mL), wide linear range (from 0.025 to 10 ng/mL), good recovery rate (92.86–103.34% in OA-spiked clam samples) and repeatability (RSD of 2.28–4.53%). The proposed method can be used to detect OA in seafood products with high sensitivity and can potentially be adapted for the determination of other small molecular analytes.
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Affiliation(s)
- Huajie Gu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liling Hao
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Ma
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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73
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Dirkzwager RM, Kinghorn AB, Richards JS, Tanner JA. APTEC: aptamer-tethered enzyme capture as a novel rapid diagnostic test for malaria. Chem Commun (Camb) 2016; 51:4697-700. [PMID: 25692283 DOI: 10.1039/c5cc00438a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report the rapid diagnosis of malaria by aptamer-tethered enzyme capture (APTEC) whereby an aptamer captures biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH) then activity is measured colorimetrically. The robust test was sensitive (limit of detection = 4.9 ng mL(-1)) and could reliably diagnose malaria in clinical blood samples.
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Affiliation(s)
- Roderick M Dirkzwager
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R..
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74
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Xenobiotic Life. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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75
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Kath-Schorr S. Cycloadditions for Studying Nucleic Acids. Top Curr Chem (Cham) 2015; 374:4. [PMID: 27572987 DOI: 10.1007/s41061-015-0004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.
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Affiliation(s)
- Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, University of Bonn, Bonn, Germany.
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76
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Hamula CLA, Peng H, Wang Z, Tyrrell GJ, Li XF, Le XC. An improved SELEX technique for selection of DNA aptamers binding to M-type 11 of Streptococcus pyogenes. Methods 2015; 97:51-7. [PMID: 26678795 DOI: 10.1016/j.ymeth.2015.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pyogenes is a clinically important pathogen consisting of various serotypes determined by different M proteins expressed on the cell surface. The M type is therefore a useful marker to monitor the spread of invasive S. pyogenes in a population. Serotyping and nucleic acid amplification/sequencing methods for the identification of M types are laborious, inconsistent, and usually confined to reference laboratories. The primary objective of this work is to develop a technique that enables generation of aptamers binding to specific M-types of S. pyogenes. We describe here an in vitro technique that directly used live bacterial cells and the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) strategy. Live S. pyogenes cells were incubated with DNA libraries consisting of 40-nucleotides randomized sequences. Those sequences that bound to the cells were separated, amplified using polymerase chain reaction (PCR), purified using gel electrophoresis, and served as the input DNA pool for the next round of SELEX selection. A specially designed forward primer containing extended polyA20/5Sp9 facilitated gel electrophoresis purification of ssDNA after PCR amplification. A counter-selection step using non-target cells was introduced to improve selectivity. DNA libraries of different starting sequence diversity (10(16) and 10(14)) were compared. Aptamer pools from each round of selection were tested for their binding to the target and non-target cells using flow cytometry. Selected aptamer pools were then cloned and sequenced. Individual aptamer sequences were screened on the basis of their binding to the 10 M-types that were used as targets. Aptamer pools obtained from SELEX rounds 5-8 showed high affinity to the target S. pyogenes cells. Tests against non-target Streptococcus bovis, Streptococcus pneumoniae, and Enterococcus species demonstrated selectivity of these aptamers for binding to S. pyogenes. Several aptamer sequences were found to bind preferentially to the M11 M-type of S. pyogenes. Estimated binding dissociation constants (Kd) were in the low nanomolar range for the M11 specific sequences; for example, sequence E-CA20 had a Kd of 7±1 nM. These affinities are comparable to those of a monoclonal antibody. The improved bacterial cell-SELEX technique is successful in generating aptamers selective for S. pyogenes and some of its M-types. These aptamers are potentially useful for detecting S. pyogenes, achieving binding profiles of the various M-types, and developing new M-typing technologies for non-specialized laboratories or point-of-care testing.
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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, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta 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, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Gregory J Tyrrell
- The Provincial Laboratory for Public Health for Alberta, Walter Mackenzie Health Sciences Centre, Edmonton, Alberta T6G 2J2, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, 2B3.12 Walter Mackenzie Health Sciences Centre, Edmonton, Alberta T6G 2B7, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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Huang SS, Wei SC, Chang HT, Lin HJ, Huang CC. Gold nanoparticles modified with self-assembled hybrid monolayer of triblock aptamers as a photoreversible anticoagulant. J Control Release 2015; 221:9-17. [PMID: 26643617 DOI: 10.1016/j.jconrel.2015.11.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/04/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023]
Abstract
We demonstrated that thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs), prepared from a self-assembled hybrid monolayer (SAHM) of triblock aptamers on Au NPs (13 nm), can effectively inhibit thrombin activity toward fibrinogen. The first block poly(adenine) at the end of the triblock TBA was used for the self-assembly on Au NP surface. The second block, in the middle of TBA, was composed of oligonucleotides that could hybridize with each other. The third block, containing TBA15 (15-base, binding to the exosite I of thrombin) and TBA29 (29-base, binding to the exosite II of thrombin) provided bivalent interaction with thrombin. The SAHM triblock aptamers have optimal distances between TBA15 and TBA29, aptamer density, and orientation on the Au NP surfaces. These properties strengthen the interactions with thrombin (Kd=1.5 × 10(-11)M), resulting in an extremely high anticoagulant potency. The thrombin clotting time mediated by SAHM TBA15/TBA29-Au NPs was >10 times longer than that of four commercially available drugs (heparin, argatroban, hirudin, or warfarin). In addition, the rat-tail bleeding assay time further demonstrated that the SAHM TBA15/TBA29-Au NPs were superior to heparin. The SAHM TBA15/TBA29-Au NPs exhibited excellent stability in the human plasma (half-life >14 days) and good biocompatibility (low cytotoxicity and hemolysis). Most interestingly, the inhibition by SAHM TBA15/TBA29-Au NPs was controllable by the irradiation of green laser, via heat transfer-induced TBA release from Au NPs. Therefore, these easily prepared (self-assembled), low cost (non-thiolated aptamer), photo-controllable, multivalent TBA15/TBA29-Au NPs (high density of TBA15/TBA29 on Au NPs) show good potential for the treatment of various diseases related to blood-clotting disorders. Our study opens up the possibility of regulation of molecule binding, protein recognition, and enzyme activity using SAHM aptamer-functionalized nanomaterials.
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Affiliation(s)
- San-Shan Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Shih-Chun Wei
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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78
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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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79
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McKeague M, De Girolamo A, Valenzano S, Pascale M, Ruscito A, Velu R, Frost NR, Hill K, Smith M, McConnell EM, DeRosa MC. Comprehensive analytical comparison of strategies used for small molecule aptamer evaluation. Anal Chem 2015; 87:8608-12. [PMID: 26192270 DOI: 10.1021/acs.analchem.5b02102] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are versatile molecular recognition agents that bind to their targets with high selectivity and affinity. The past few years have seen a dramatic increase in aptamer development and interest for diagnostic and therapeutic applications. As the applications for aptamers expand, the need for a more standardized, stringent, and informative characterization and validation methodology increases. Here we performed a comprehensive analysis of a panel of conventional affinity binding assays using a suite of aptamers for the small molecule target ochratoxin A (OTA). Our results highlight inconsistency between conventional affinity assays and the need for multiple characterization strategies. To mitigate some of the challenges revealed in our head-to-head comparison of aptamer binding assays, we further developed and evaluated a set of novel strategies that facilitate efficient screening and characterization of aptamers in solution. Finally, we provide a workflow that permits rapid and robust screening, characterization, and functional verification of aptamers thus improving their development and integration into novel applications.
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Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University , 443 Via Ortega, Stanford, California 94305, United States
| | - Annalisa De Girolamo
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Stefania Valenzano
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Michelangelo Pascale
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Annamaria Ruscito
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Ranganathan Velu
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Nadine R Frost
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Kayla Hill
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - McKenzie Smith
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Erin M McConnell
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Maria C DeRosa
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
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80
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Mao Y, Liu M, Tram K, Gu J, Salena BJ, Jiang Y, Li Y. Optimal DNA templates for rolling circle amplification revealed by in vitro selection. Chemistry 2015; 21:8069-74. [PMID: 25877998 DOI: 10.1002/chem.201500994] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/21/2023]
Abstract
Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing.
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Affiliation(s)
- Yu Mao
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).,The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055 (P. R. China)
| | - Meng Liu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Kha Tram
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Jimmy Gu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).
| | - Yingfu Li
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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81
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Jo H, Her J, Ban C. Dual aptamer-functionalized silica nanoparticles for the highly sensitive detection of breast cancer. Biosens Bioelectron 2015; 71:129-136. [PMID: 25897882 DOI: 10.1016/j.bios.2015.04.030] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/26/2015] [Accepted: 04/12/2015] [Indexed: 02/07/2023]
Abstract
In this study, we synthesized dual aptamer-modified silica nanoparticles that simultaneously target two types of breast cancer cells: the mucin 1 (MUC1)(+) and human epidermal growth factor receptor 2 (HER2)(+) cell lines. Dual aptamer system enables a broad diagnosis for breast cancer in comparison with the single aptamer system. The dye-doped silica nanoparticles offer great stability with respect to photobleaching and enable the accurate quantification of breast cancer cells. The morphological and spectroscopic characteristics of the designed Dual-SiNPs were demonstrated via diverse methods such as DLS, zeta potential measurements, UV-vis spectroscopy, and fluorescence spectroscopy. Negatively charged Dual-SiNPs with a homogeneous size distribution showed robust and strong fluorescence. In addition, Dual-SiNPs did not affect cell viability, implying that this probe might be readily available for use in an in vivo system. Through ratio optimization of the MUC1 and HER2 aptamers, the binding capacities of the Dual-SiNPs to both cell lines were maximized. Based on Dual-SiNPs, a highly sensitive quantification of breast cancer cells was performed, resulting in a detection limit of 1 cell/100 μL, which is significantly lower compared with those reported in other studies. Moreover, the developed detection platform displayed high selectivity for only the MUC1(+) and HER2(+) cell lines. It is expected that this valuable diagnostic probe will be a noteworthy platform for the diagnosis and prognosis of breast cancer.
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Affiliation(s)
- Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Jin Her
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 790-784, South Korea.
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