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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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2
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Taneja V, Goel M, Shankar U, Kumar A, Khilnani GC, Prasad HK, Prasad GBKS, Gupta UD, Sharma TK. An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients. ACS COMBINATORIAL SCIENCE 2020; 22:656-666. [PMID: 33063508 DOI: 10.1021/acscombsci.0c00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dysregulation of IFN-α is the basis for pathogenesis of autoimmune as well as infectious diseases. Identifying inflammatory signatures in peripheral blood of patients is an approach for monitoring active infection. Hence, estimation of type I IFNs as an inflammatory biomarker to scrutinize disease status after treatment is useful. Accordingly, an Aptamer Linked Immobilized Sorbent Assay (ALISA) for the detection of IFN-α in serum samples was developed. Sixteen aptamers were screened for their ability to bind IFN-α. Aptamer IFNα-3 exhibited specificity for IFN-α with no cross-reactivity with interferons β and γ and human serum albumin. The disassociation constant (Kd) was determined to be 3.96 ± 0.36 nM, and the limit of detection was ∼2 ng. The characterized IFNα-3 aptamer was used in ALISA to screen tuberculosis (TB) patients' sera. An elevated IFN-α level in sera derived from untreated TB patients (median = 0.31), compared to nontuberculous household contacts (median = 0.13) and healthy volunteers (median = 0.12), and further a decline in IFN-α level among treated patients (median = 0.13) were seen. The ALISA assay facilitates direct estimation of inflammatory protein(s) in circulation unlike mRNA estimation by real time PCR. Designing of aptamers similar to the IFNα-3 aptamer provides a novel approach to assess other inflammatory protein(s) in patients before, during, and after completion of treatment and would denote clinical improvement in successfully treated patients.
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Affiliation(s)
- Vibha Taneja
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
- Department of Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh 474011, India
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manish Goel
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Gopi C. Khilnani
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Hanumanthappa K. Prasad
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | | | - Umesh D. Gupta
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
| | - Tarun K. Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
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3
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Bialy RM, Ali MM, Li Y, Brennan JD. Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer. Chemistry 2020; 26:5085-5092. [PMID: 32096262 DOI: 10.1002/chem.202000245] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/21/2020] [Indexed: 12/22/2022]
Abstract
We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.
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Affiliation(s)
- Roger M Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Monsur M Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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4
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Cao C, Zhang F, Goldys EM, Gao F, Liu G. Advances in structure-switching aptasensing towards real time detection of cytokines. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Razmi N, Baradaran B, Hejazi M, Hasanzadeh M, Mosafer J, Mokhtarzadeh A, de la Guardia M. Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor. Biosens Bioelectron 2018; 113:58-71. [PMID: 29729560 DOI: 10.1016/j.bios.2018.04.048] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 01/13/2023]
Abstract
Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional methods for PDGF-BB detection, requiring high-cost and complicated instrumentation, take too much time and offer deficient sensitivity and selectivity, which restrict their usage in real applications. Hence, it is essential to design and build enhanced systems and platforms for the recognition and quantification of protein biomarkers. In the past few years, biosensors especially aptasensors have been received noticeable attention for the detection of PDGF-BB owing to their high sensitivity, selectivity, accuracy, fast response, and low cost. Since the role and importance of developing aptasensors in cancer diagnosis is undeniable. In this review, optical and electrochemical aptasensors, which have been applied by many researchers for PDGF-BB cancer biomarker detection, have been mentioned and merits and demerits of them have been explained and compared. Efforts related to design and development of aptamer-based biosensors using nanoparticles for sensitive and selective detection of PDGF-BB have been reviewed considering: Aptamer importance as recognition elements, principal, application and the recent improvements and developments of aptamer based optical and electrochemical methods. In addition, commercial biosensors and future perspectives for rapid and on-site detection of PDGF-BB have been summarized.
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Affiliation(s)
- Nasrin Razmi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz 51664 Iran
| | - Jafar Mosafer
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran.
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
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6
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Jiang LF, Chen BC, Chen B, Li XJ, Liao HL, Zhang WY, Wu L. Aptamer-functionalized Fe 3 O 4 magnetic nanoparticles as a solid-phase extraction adsorbent for the selective extraction of berberine from Cortex phellodendri. J Sep Sci 2017; 40:2933-2940. [PMID: 28556490 DOI: 10.1002/jssc.201700103] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/12/2017] [Accepted: 05/20/2017] [Indexed: 11/11/2022]
Abstract
The extraction adsorbent was fabricated by immobilizing the highly specific recognition and binding of aptamer onto the surface of Fe3 O4 magnetic nanoparticles, which not only acted as recognition elements to recognize and capture the target molecule berberine from the extract of Cortex phellodendri, but also could favor the rapid separation and purification of the bound berberine by using an external magnet. The developed solid-phase extraction method in this work was useful for the selective extraction and determination of berberine in Cortex phellodendri extracts. Various conditions such as the amount of aptamer-functionalized Fe3 O4 magnetic nanoparticles, extraction time, temperature, pH value, Mg2+ concentration, elution time and solvent were optimized for the solid-phase extraction of berberine. Under optimal conditions, the purity of berberine extracted from Cortex phellodendri was as high as 98.7% compared with that of 4.85% in the extract, indicating that aptamer-functionalized Fe3 O4 magnetic nanoparticles-based solid-phase extraction method was very effective for berberine enrichment and separation from a complex herb extract. The applicability and reliability of the developed solid-phase extraction method were demonstrated by separating berberine from nine different concentrations of one Cortex phellodendri extract. The relative recoveries of the spiked solutions of all the samples were between 95.4 and 111.3%, with relative standard deviations ranging between 0.57 and 1.85%.
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Affiliation(s)
- Ling-Feng Jiang
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Bo-Cheng Chen
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Ben Chen
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Xue-Jian Li
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Hai-Lin Liao
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Wen-Yan Zhang
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
| | - Lin Wu
- Guangxi Scientific Research Centre of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, PR China.,Guangxi Key Laboratory of Chinese Medicine Foundation Research, Guangxi University of Chinese Medicine, Nanning, PR China
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7
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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8
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Bioengineering tools to elucidate and control the fate of transplanted stem cells. Biochem Soc Trans 2015; 42:679-87. [PMID: 24849237 DOI: 10.1042/bst20130276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For the last decade, stem cell therapies have demonstrated enormous potential for solving some of the most tragic illnesses, diseases and tissue defects worldwide. Currently, more than 1300 clinical trials use stem cell therapy to solve a spectrum of cardiovascular, neurodegenerative and autoimmune diseases (http://www.clinicaltrials.gov, Jan 2014, search term: stem cell therapy; only currently recruiting and completed studies are included in the search). However, the efficacy of stem cell transplantation in patients has not been well established, and recent clinical trials have produced mixed results. We attribute this lack of efficacy in part to an incomplete understanding of the fate of stem cells following transplantation and the lack of control over cell fate, especially cell-homing and therapeutic functions. In the present review, we present two of our recently developed technologies that aim to address the above-mentioned bottlenecks in stem cell therapy specifically in the areas of MSCs (mesenchymal stem cells): (i) aptamer-based cell-surface sensors to study cellular microenvironments, and (ii) mRNA engineering technology to enhance the homing and immunomodulatory efficacy of transplanted stem cells. The first engineering strategy aims to elucidate the basic cellular signalling that occurs in the microenvironment of transplanted stem cells in real time. The second technique involves a simple mRNA transfection that improves the homing and anti-inflammatory capability of MSCs. Although we have specifically applied these engineering techniques to MSCs, these strategies can be incorporated for almost any cell type to determine and control the fate of transplanted stem cells.
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Stenken JA, Poschenrieder AJ. Bioanalytical chemistry of cytokines--a review. Anal Chim Acta 2015; 853:95-115. [PMID: 25467452 PMCID: PMC4717841 DOI: 10.1016/j.aca.2014.10.009] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.
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Affiliation(s)
- Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andreas J Poschenrieder
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Pharmaceutical Radiochemistry, Technische Universität München, Walther-Meißner-Street 3, D-85748 Garching, Germany
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10
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Wiraja C, Yeo D, Lio D, Labanieh L, Lu M, Zhao W, Xu C. Aptamer technology for tracking cells' status & function. MOLECULAR AND CELLULAR THERAPIES 2014; 2:33. [PMID: 26056599 PMCID: PMC4452066 DOI: 10.1186/2052-8426-2-33] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023]
Abstract
In fields such as cancer biology and regenerative medicine, obtaining information regarding cell bio-distribution, tropism, status, and other cellular functions are highly desired. Understanding cancer behaviors including metastasis is important for developing effective cancer treatments, while assessing the fate of therapeutic cells following implantation is critical to validate the efficacy and efficiency of the therapy. For visualization purposes with medical imaging modalities (e.g. magnetic resonance imaging), cells can be labeled with contrast agents (e.g. iron-oxide nanoparticles), which allows their identification from the surrounding environment. Despite the success of revealing cell biodistribution in vivo, most of the existing agents do not provide information about the status and functions of cells following transplantation. The emergence of aptamers, single-stranded RNA or DNA oligonucleotides of 15 to 60 bases in length, is a promising solution to address this need. When aptamers bind specifically to their cognate molecules, they undergo conformational changes which can be transduced into a change of imaging contrast (e.g. optical, magnetic resonance). Thus by monitoring this signal change, researchers can obtain information about the expression of the target molecules (e.g. mRNA, surface markers, cell metabolites), which offer clues regarding cell status/function in a non-invasive manner. In this review, we summarize recent efforts to utilize aptamers as biosensors for monitoring the status and function of transplanted cells. We focus on cancer cell tracking for cancer study, stem cell tracking for regenerative medicine, and immune cell (e.g. dendritic cells) tracking for immune therapy.
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Affiliation(s)
- Christian Wiraja
- />Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457 Singapore
| | - David Yeo
- />Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457 Singapore
| | - Daniel Lio
- />Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457 Singapore
| | - Louai Labanieh
- />Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697 USA
- />Department of Biomedical Engineering, Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, CA 92697 USA
| | - Mengrou Lu
- />Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697 USA
- />Department of Biomedical Engineering, Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, CA 92697 USA
| | - Weian Zhao
- />Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92697 USA
- />Department of Biomedical Engineering, Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California Irvine, Irvine, CA 92697 USA
| | - Chenjie Xu
- />Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457 Singapore
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Jun J, Lee JS, Shin DH, Jang J. Aptamer-functionalized hybrid carbon nanofiber FET-type electrode for a highly sensitive and selective platelet-derived growth factor biosensor. ACS APPLIED MATERIALS & INTERFACES 2014; 6:13859-13865. [PMID: 25020238 DOI: 10.1021/am5032693] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Precise selectivity and rapid responses to target biomolecules are important in the development of biosensors. In particular, highly sensitive and selective biosensors have been used in clinical treatment to detect factors such as cancer oncoproteins and endocrine disruptors. Herein, highly sensitive liquid electrolyte field-effect transistor (FET) system biosensors were fabricated to detect platelet-derived growth factor (PDGF) using a PDGF-B binding aptamer conjugated with carboxylic polypyrrole-coated metal oxide-decorated carbon nanofibers (CPMCNFs) as the signal transducer. First, CPMCNFs were fabricated using vapor deposition polymerization (VDP) of the carboxylic pryrrole monomer (CPy) on metal oxide-decorated carbon nanofiber (MCNF) surfaces with no treatment for carbon surface functionalization. Furthermore, a 3 nm thick uniformly coated carboxylic polypyrrole (CPPy) layer was formed without aggregation. The CPMCNFs were integrated with the PDGF-B binding aptamer and immobilized on the interdigitated array substrate by covalent anchoring to produce a FET-type biosensor transducer. The PDGF-B binding aptamer conjugated CPMCNF (CPB-Apt) FET sensor was highly sensitive (5 fM) and extremely selective for isoforms of PDGFs. Additionally, the CPB-Apt FET sensor could be reused over a few weeks.
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Affiliation(s)
- Jaemoon Jun
- School of Chemical and Biological Engineering, College of Engineering, Seoul National University (SNU) , 599 Gwanangno, Gwanak-gu, Seoul, 151-742 Korea
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Wang Q, Zheng H, Gao X, Lin Z, Chen G. A label-free ultrasensitive electrochemical aptameric recognition system for protein assay based on hyperbranched rolling circle amplification. Chem Commun (Camb) 2014; 49:11418-20. [PMID: 24169529 DOI: 10.1039/c3cc46274a] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free ultrasensitive electrochemical aptameric sensor which combined the advantages of an aptamer and hyperbranched rolling circle amplification (HRCA) has been developed for specific recognition of a platelet-derived growth factor B-chain (PDGF-BB).
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Affiliation(s)
- Qingping Wang
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China
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13
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Päkkilä H, Blom S, Kopra K, Soukka T. Aptamer-directed lanthanide chelate self-assembly for rapid thrombin detection. Analyst 2014; 138:5107-12. [PMID: 23807946 DOI: 10.1039/c3an00192j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a sensitive assay method for homogeneous thrombin detection. The method is based on lanthanide chelate complementation, where the luminescent complex is split into two separate label moieties, which are intrinsically non-luminescent. A luminescent mixed chelate complex is formed only when the label moieties are brought into close proximity directed by two separate binding events of aptamers to the analyte. This results in high specificity in signal generation while time-resolved fluorescence detection eliminates the short lifetime autofluorescence, which is inherent to many homogeneous assays and limits their applicability. The developed method is also very rapid as the maximum signal is obtained in just five minutes. Lanthanide chelate complementation can be applied for the detection of other proteins when two binders recognizing separate epitopes of the analyte are available.
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Affiliation(s)
- Henna Päkkilä
- Department of Biotechnology, University of Turku, Tykistökatu 6 A 6th floor, FI-20520 Turku, Finland.
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14
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Hill EH, Evans DG, Whitten DG. The influence of structured interfacial water on the photoluminescence of carboxyester-terminated oligo-p-phenylene ethynylenes. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eric H. Hill
- Center for Biomedical Engineering, Department of Chemical and Nuclear Engineering; University of New Mexico; Albuquerque NM 87131-1341 USA
- The Nanoscience and Microsystems Engineering Program and Department of Chemistry and Chemical Biology; University of New Mexico; Albuquerque NM 87131-1341 USA
| | - Deborah G. Evans
- The Nanoscience and Microsystems Engineering Program and Department of Chemistry and Chemical Biology; University of New Mexico; Albuquerque NM 87131-1341 USA
| | - David G. Whitten
- Center for Biomedical Engineering, Department of Chemical and Nuclear Engineering; University of New Mexico; Albuquerque NM 87131-1341 USA
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16
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Bosco F, Bache M, Yang J, Chen C, Hwu ET, Lin Q, Boisen A. Micromechanical PDGF recognition via lab-on-a-disc aptasensor arrays. SENSORS AND ACTUATORS. A, PHYSICAL 2013; 195:154-159. [PMID: 24672146 PMCID: PMC3963500 DOI: 10.1016/j.sna.2012.06.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A plug-and-play CD-like platform is used to perform a statistical detection of platelet derived growth factor (PDGF) proteins through aptamer-based surface functionalization of multiple microcantilever arrays. When PDGF proteins bind to aptamer coatings, the cantilevers deflect. The deflection response is monitored by optical read-out units from a commercial DVD-ROM device. We report on the use of an improved sensing platform which facilitates measurements under continuous liquid flow and with temperature control. Also, the mechanical wobbling of the DVD-ROM platform has been minimized and the scanning system has been optimized in order to detect cantilever deflections in liquid with nanometer scale resolution. The capability of the sensing platform is demonstrated by detection of clinically relevant concentrations of PDGF proteins. We present statistical measurements on 100 microcantilevers at different concentrations of PDGF, ranging from 10 nM to 400 nM. Hereby it is possible to reliably characterize the averaged mechanical response of cantilevers as a function of protein concentration.
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Affiliation(s)
- F.G. Bosco
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - M. Bache
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
| | - J. Yang
- Department of Mechanical Engineering, Columbia University, New York 10027, NY, United States
| | - C.H. Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - E.-T. Hwu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Q. Lin
- Department of Mechanical Engineering, Columbia University, New York 10027, NY, United States
| | - A. Boisen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby 2800, Denmark
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17
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Fu H, Ge C, Cheng W, Luo C, Zhang D, Yan L, He Y, Yi G. A Hairpin Electrochemical Aptasensor for Sensitive and Specific Detection of Thrombin Based on Homogenous Target Recognition. ELECTROANAL 2013. [DOI: 10.1002/elan.201200506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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19
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Penmatsa V, Ruslinda AR, Beidaghi M, Kawarada H, Wang C. Platelet-derived growth factor oncoprotein detection using three-dimensional carbon microarrays. Biosens Bioelectron 2012; 39:118-23. [PMID: 22841446 DOI: 10.1016/j.bios.2012.06.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/13/2012] [Accepted: 06/29/2012] [Indexed: 01/31/2023]
Abstract
The potential of aptamers as ligand binding molecule has opened new avenues in the development of biosensors for cancer oncoproteins. In this paper, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor (PDGF-BB) oncoprotein detection is reported. The detection mechanism is based on the release of fluorophore (TOTO intercalating dye) from the target binding aptamer's stem structure when it captures PDGF. Amino-terminated three-dimensional carbon microarrays fabricated by pyrolyzing patterned photoresist were used as a detection platform. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5pmol. This detection strategy is promising in a wide range of applications in the detection of cancer biomarkers and other proteins.
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Affiliation(s)
- Varun Penmatsa
- Department of Mechanical and Materials Engineering, Florida International University, United States
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20
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Ali MM, Kang DK, Tsang K, Fu M, Karp JM, Zhao W. Cell-surface sensors: lighting the cellular environment. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 4:547-61. [PMID: 22761045 DOI: 10.1002/wnan.1179] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-surface sensors are powerful tools to elucidate cell functions including cell signaling, metabolism, and cell-to-cell communication. These sensors not only facilitate our understanding in basic biology but also advance the development of effective therapeutics and diagnostics. While genetically encoded fluorescent protein/peptide sensors have been most popular, emerging cell surface sensor systems including polymer-, nanoparticle-, and nucleic acid aptamer-based sensors have largely expanded our toolkits to interrogate complex cellular signaling and micro- or nano-environments. In particular, cell-surface sensors that interrogate in vivo cellular microenvironments represent an emerging trend in the development of next generation tools which biologists may routinely apply to elucidate cell biology in vivo and to develop new therapeutics and diagnostics. This review focuses on the most recent development in areas of cell-surface sensors. We will first discuss some recently reported genetically encoded sensors that were used for monitoring cellular metabolites, proteins, and neurotransmitters. We will then focus on the emerging cell surface sensor systems with emphasis on the use of DNA aptamer sensors for probing cell signaling and cell-to-cell communication.
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Affiliation(s)
- Md Monsur Ali
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
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21
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Citartan M, Gopinath SCB, Tominaga J, Tan SC, Tang TH. Assays for aptamer-based platforms. Biosens Bioelectron 2012; 34:1-11. [PMID: 22326894 DOI: 10.1016/j.bios.2012.01.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 12/14/2011] [Accepted: 01/06/2012] [Indexed: 11/19/2022]
Abstract
Aptamers are single stranded DNA or RNA oligonucleotides that have high affinity and specificity towards a wide range of target molecules. Aptamers have low molecular weight, amenable to chemical modifications and exhibit stability undeterred by repetitive denaturation and renaturation. Owing to these indispensable advantages, aptamers have been implemented as molecular recognition element as alternative to antibodies in various assays for diagnostics. By amalgamating with a number of methods that can provide information on the aptamer-target complex formation, aptamers have become the elemental tool for numerous biosensor developments. In this review, administration of aptamers in applications involving assays of fluorescence, electrochemistry, nano-label and nano-constructs are discussed. Although detection strategies are different for various aptamer-based assays, the core of the design strategies is similar towards reporting the presence of specific target binding to the corresponding aptamers. It is prognosticated that aptamers will find even broader applications with the development of new methods of transducing aptamer target binding.
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Affiliation(s)
- Marimuthu Citartan
- Infectious Disease Cluster, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
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22
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Zhang ZZ, Zhang CY. Highly sensitive detection of protein with aptamer-based target-triggering two-stage amplification. Anal Chem 2012; 84:1623-9. [PMID: 22224936 DOI: 10.1021/ac2029002] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Highly sensitive detection of proteins is essential to biomedical research as well as clinical diagnosis. However, so far most detection methods rely on antibody-based assays and are usually laborious and time-consuming with poor sensitivity. Here, we develop a simple and sensitive method for the detection of a biomarker protein, platelet-derived growth factor BB (PDGF-BB), based on aptamer-based target-triggering two-stage amplification. With the involvement of an aptamer-based probe and an exponential amplification reaction (EXPAR) template, our method combines strand displacement amplification (SDA) and EXPAR, transforming the probe conformational change induced by target binding into two-stage amplification and distinct fluorescence signal. This detection method exhibits excellent specificity and high sensitivity with a detection limit of 9.04 × 10(-13) M and a detection range of more than 5 orders of magnitude, which is comparable with or even superior to most currently used approaches for PDGF-BB detection. Moreover, this detection method has significant advantages of isothermal conditions required, simple and rapid without multiple separation and washing steps, low-cost without the need of any labeled DNA probes. Furthermore, this method might be extended to sensitive detection of a variety of biomolecules whose aptamers undergo similar conformational changes.
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Affiliation(s)
- Zhen-zhu Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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23
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Kiy MM, Jacobi ZE, Liu J. Metal-induced specific and nonspecific oligonucleotide folding studied by FRET and related biophysical and bioanalytical implications. Chemistry 2011; 18:1202-8. [PMID: 22180064 DOI: 10.1002/chem.201102515] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Indexed: 01/12/2023]
Abstract
Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, nonspecific folding induced by mono- or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg(II) binding DNA and monitored metal-induced folding in the presence of various cations. While nonspecific electrostatically mediated folding can be very significant, at each tested salt condition, Hg(II) induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signal the formation of double-stranded DNA showed a lower dependency on ionic strength.
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Affiliation(s)
- Mehmet Murat Kiy
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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24
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Crisalli P, Kool ET. Multi-path quenchers: efficient quenching of common fluorophores. Bioconjug Chem 2011; 22:2345-54. [PMID: 22034828 DOI: 10.1021/bc200424r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescence quenching groups are widely employed in biological detection, sensing, and imaging. To date, a relatively small number of such groups are in common use. Perhaps the most commonly used quencher, dabcyl, has limited efficiency with a broad range of fluorophores. Here, we describe a molecular approach to improve the efficiency of quenchers by increasing their electronic complexity. Multi-Path Quenchers (MPQ) are designed to have multiple donor or acceptor groups in their structure, allowing for a multiplicity of conjugation pathways of varied length. This has the effect of broadening the absorption spectrum, which in turn can increase quenching efficiency and versatility. Six such MPQ derivatives are synthesized and tested for quenching efficiency in a DNA hybridization context. Duplexes placing quenchers and fluorophores within contact distance or beyond this distance are used to measure quenching via contact or FRET mechanisms. Results show that several of the quenchers are considerably more efficient than dabcyl at quenching a wider range of common fluorophores, and two quench fluorescein and TAMRA as well as or better than a Black Hole Quencher.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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25
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Lin TE, Chen WH, Shiang YC, Huang CC, Chang HT. Colorimetric detection of platelet-derived growth factors through competitive interactions between proteins and functional gold nanoparticles. Biosens Bioelectron 2011; 29:204-9. [PMID: 21900002 DOI: 10.1016/j.bios.2011.08.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/09/2011] [Accepted: 08/15/2011] [Indexed: 01/09/2023]
Abstract
We have developed a colorimetric assay-using aptamer modified 13-nm gold nanoparticles (Apt-Au NPs) and fibrinogen adsorbed Au NPs (Fib-Au NPs, 56nm)-for the highly selective and sensitive detection of platelet-derived growth factors (PDGF). Apt-Au NPs and Fib-Au NPs act as recognition and reporting units, respectively. PDGF-binding-aptamer (Apt(PDGF)) and 29-base-long thrombin-binding-aptamer (Apt(thr29)) are conjugated with Au NPs to prepare functional Apt-Au NPs (Apt(PDGF)/Apt(thr29)-Au NPs) for specific interaction with PDGF and thrombin, respectively. Thrombin interacts with Fib-Au NPs in solutions to catalyze the formation of insoluble fibrillar fibrin-Au NPs agglutinates through the polymerization of the unconjugated and conjugated fibrinogen. The activity of thrombin is suppressed once it interacts with the Apt(PDGF)/Apt(thr29)-Au NPs. The suppression decreases due to steric effects through the specific interaction of PDGF with Apt(PDGF), occurring on the surfaces of Apt(PDGF)/Apt(thr29)-Au NPs. Under optimal conditions [Apt(PDGF)/Apt(thr29)-Au NPs (25pM), thrombin (400pM) and Fib-Au NPs (30pM)], the Apt(PDGF)/Apt(thr29)-Au NPs/Fib-Au NPs probe responds linearly to PDGF over the concentration range of 0.5-20nM with a correlation coefficient of 0.96. The limit of detection (LOD, signal-to-noise ratio=3) for each of the three PDGF isoforms is 0.3nM in the presence of bovine serum albumin at 100μM. When using the Apt(PDGF)/Apt(thr29)-Au NPs as selectors for the enrichment of PDGF and for the removal of interferences from cell media, the LOD for PDGF provided by this probe is 35pM. The present probe reveals that the concentration of PDGF in the three cell media is 230 (±20)pM, showing its advantages of simplicity, sensitivity, and specificity.
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Affiliation(s)
- Tzu-En Lin
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan
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26
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He Y, Wang ZG, Tang HW, Pang DW. Low background signal platform for the detection of ATP: when a molecular aptamer beacon meets graphene oxide. Biosens Bioelectron 2011; 29:76-81. [PMID: 21889887 DOI: 10.1016/j.bios.2011.07.069] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/23/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
Abstract
A novel molecular aptamer beacon (MAB) was designed by integrating a single-labeled hairpin-shaped aptamer and graphene oxide (GO). The hairpin-shaped aptamer was constructed with anti-ATP aptamer and another five nucleotides added to the 5'-end of the aptamer which are complementary to nucleotides at the 3'-end of the aptamer to form a hairpin-shaped probe. This newly designed MAB which acts as a low background signal platform was used for the ATP detection based on long-range resonance energy transfer (LrRET). In the absence of ATP, the adsorption of the dye-labeled hairpin-shaped aptamer on GO makes the dyes close proximity to GO surface resulting in high efficiency quenching of fluorescence of the dyes. Therefore, the fluorescence of the designed MAB is completely quenched by GO, and the system shows very low background. Conversely, and very importantly, upon the adding of ATP, the quenched fluorescence is recovered significantly, and ATP can be detected in a wide range of 5-2500μM with a detection limit of 2μM and good selectivity. Moreover, when the GO-based MAB was used in cellular ATP assays, preeminent fluorescence signals were obtained, thus the platform of GO-based MAB could be used to detect ATP in real-world samples.
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Affiliation(s)
- Yue He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Research Center for Nanobiology and Nanomedicine (MOE 985 Innovative Platform), Wuhan Institute of Biotechnology, Wuhan University, Wuhan, 430072, PR China
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27
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Feng K, Qiu LP, Yang Y, Wu ZS, Shen GL, Yu RQ. Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers. Biosens Bioelectron 2011; 29:66-75. [PMID: 21872459 DOI: 10.1016/j.bios.2011.07.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 07/19/2011] [Accepted: 07/27/2011] [Indexed: 02/02/2023]
Abstract
Oligonucleotide-based detection schemes that avoid chemical modification possess significant advantages, including simplified design, intrinsic affinity for targets, low cost and ease to extend applications. In this contribution, we developed a label-free self-locked bifunctional oligonucleotide probe (signaling probe) for the detection of different disease markers in parallel. Two signal enhancement techniques based on isothermal circular strand-displacement polymerization reaction, cyclical nucleic acid strand-displacement polymerization (CNDP) and cyclical common (nonnucleic acid) target-displacement polymerization (CCDP), were employed to implement the amplification assay for p53 gene and PDGF-BB, respectively. The attractive assay properties confirmed the effectiveness of isothermal polymerization in common biosensing systems without evolving any chemical modification: PDGF could be detected down to 0.87ng/mL, and a dynamic response range of 8-5000ng/mL was achieved; The capability to screen the p53 gene was also considerably improved, including the detection limit, sensitivity, dynamic range and so on. Moreover, because no any chemical modification of the signaling probe was acquired and different targets were separately detected in homogeneous solution. This interrogating platform exhibits the design flexibility, convenience, simplicity and cost-effectiveness. The success achieved here is expected to serve as a significant step toward the development of robust label-free oligonucleotide probes in biomarker profiling and disease diagnostics.
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Affiliation(s)
- Kejun Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, PR China
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28
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Cao ZJ, Peng QW, Qiu X, Liu CY, Lu JZ. Highly sensitive chemiluminescence technology for protein detection using aptamer-based rolling circle amplification platform. J Pharm Anal 2011; 1:159-165. [PMID: 29403694 PMCID: PMC5760798 DOI: 10.1016/j.jpha.2011.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 06/09/2011] [Indexed: 11/30/2022] Open
Abstract
A robust, selective and highly sensitive chemiluminescent (CL) platform for protein assay was presented in this paper. This novel CL approach utilized rolling circle amplification (RCA) as a signal enhancement technique and the 96-well plate as the immobilization and separation carrier. Typically, the antibody immobilized on the surface of 96-well plate was sandwiched with the protein target and the aptamer–primer sequence. This aptamer–primer sequence was then employed as the primer of RCA. Based on this design, a number of the biotinylated probes and streptavidin–horseradish peroxidase (SA–HRP) were captured on the plate, and the CL signal was amplified. In summary, our results demonstrated a robust biosensor with a detection limit of 10 fM that is easy to be established and utilized, and devoid of light source. Therefore, this new technique will broaden the perspective for future development of DNA-based biosensors for the detection of other protein biomarkers related to clinical diseases, by taking advantages of high sensitivity and selectivity.
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Affiliation(s)
- Zhi-Juan Cao
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qian-Wen Peng
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xue Qiu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Cai-Yun Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jian-Zhong Lu
- School of Pharmacy, Fudan University, Shanghai 201203, China
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29
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Zhao W, Schafer S, Choi J, Yamanaka YJ, Lombardi ML, Bose S, Carlson AL, Phillips JA, Teo W, Droujinine IA, Cui CH, Jain RK, Lammerding J, Love JC, Lin CP, Sarkar D, Karnik R, Karp JM. Cell-surface sensors for real-time probing of cellular environments. NATURE NANOTECHNOLOGY 2011; 6:524-31. [PMID: 21765401 PMCID: PMC3163485 DOI: 10.1038/nnano.2011.101] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 06/02/2011] [Indexed: 05/16/2023]
Abstract
The ability to explore cell signalling and cell-to-cell communication is essential for understanding cell biology and developing effective therapeutics. However, it is not yet possible to monitor the interaction of cells with their environments in real time. Here, we show that a fluorescent sensor attached to a cell membrane can detect signalling molecules in the cellular environment. The sensor is an aptamer (a short length of single-stranded DNA) that binds to platelet-derived growth factor (PDGF) and contains a pair of fluorescent dyes. When bound to PDGF, the aptamer changes conformation and the dyes come closer to each other, producing a signal. The sensor, which is covalently attached to the membranes of mesenchymal stem cells, can quantitatively detect with high spatial and temporal resolution PDGF that is added in cell culture medium or secreted by neighbouring cells. The engineered stem cells retain their ability to find their way to the bone marrow and can be monitored in vivo at the single-cell level using intravital microscopy.
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Affiliation(s)
- Weian Zhao
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Sebastian Schafer
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Jonghoon Choi
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Yvonne J. Yamanaka
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Maria L. Lombardi
- Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Suman Bose
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Alicia L. Carlson
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Wellman Center for Photomedicine and Center for Systems Biology, Massachusetts General Hospital/Harvard Medical School, 40 Blossom Street, Boston, Massachusetts 02114, USA
| | - Joseph A. Phillips
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Weisuong Teo
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Ilia A. Droujinine
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Cheryl H. Cui
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Rakesh K. Jain
- Edwin L. Steele Laboratory, Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, USA
| | - Jan Lammerding
- Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - J. Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Charles P. Lin
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Wellman Center for Photomedicine and Center for Systems Biology, Massachusetts General Hospital/Harvard Medical School, 40 Blossom Street, Boston, Massachusetts 02114, USA
| | - Debanjan Sarkar
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
| | - Rohit Karnik
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Jeffrey M. Karp
- Center for Regenerative Therapeutics & Department of Medicine, Brigham & Women's Hospital, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard Stem Cell Institute, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Science and Technology, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA
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30
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31
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Zhen SJ, Chen LQ, Xiao SJ, Li YF, Hu PP, Zhan L, Peng L, Song EQ, Huang CZ. Carbon nanotubes as a low background signal platform for a molecular aptamer beacon on the basis of long-range resonance energy transfer. Anal Chem 2011; 82:8432-7. [PMID: 20853851 DOI: 10.1021/ac100709s] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although holding the advantages of both an aptamer and a molecular beacon (MB), a molecular aptamer beacon (MAB) needs complicated and expensive modifications at both of its ends and usually has a high background signal because of the low energy transfer efficiency between the donor and the acceptor. To overcome these shortcomings, in this study, we develop a long-range resonance energy transfer (LrRET) system by separating the donor from the acceptor, wherein only one end of the MAB is fluorescently labeled and acts as the energy donor and multiwalled carbon nanotubes (MWCNTs) are introduced as the energy acceptor. To test the feasibility of the newly designed MAB system, adenosine triphosphate (ATP) has been employed as a proof-of-concept target. It is found that the fluorescence of the designed MAB is completely quenched by MWCNTs, supplying a very low background signal. Then the quenched fluorescence is recovered significantly with the addition of ATP, so that ATP can be detected in the range of 0.8-80 μM with a limit of detection of 0.5 μM (3σ). Compared with the conventional fluorescence resonance energy transfer, the efficiency of LrRET between the dye and MWCNTs is much higher. Since only one end of the MAB needs the modification, the present strategy is simple and cost-effective. Furthermore, the use of MWCNTs can greatly reduce the fluorescence background of the MAB and supply a high sensitivity, showing its generality for detection of a variety of targets.
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Affiliation(s)
- Shu Jun Zhen
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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Stempfer R, Syed P, Vierlinger K, Pichler R, Meese E, Leidinger P, Ludwig N, Kriegner A, Nöhammer C, Weinhäusel A. Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens. BMC Cancer 2010; 10:627. [PMID: 21078204 PMCID: PMC2995456 DOI: 10.1186/1471-2407-10-627] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022] Open
Abstract
Background The simplicity and potential of minimal invasive testing using serum from patients make auto-antibody based biomarkers a very promising tool for use in diagnostics of cancer and auto-immune disease. Although several methods exist for elucidating candidate-protein markers, immobilizing these onto membranes and generating so called macroarrays is of limited use for marker validation. Especially when several hundred samples have to be analysed, microarrays could serve as a good alternative since processing macro membranes is cumbersome and reproducibility of results is moderate. Methods Candidate markers identified by SEREX (serological identification of antigens by recombinant expression cloning) screenings of brain and lung tumour were used for macroarray and microarray production. For microarray production recombinant proteins were expressed in E. coli by autoinduction and purified His-tag (histidine-tagged) proteins were then used for the production of protein microarrays. Protein arrays were hybridized with the serum samples from brain and lung tumour patients. Result Methods for the generation of microarrays were successfully established when using antigens derived from membrane-based selection. Signal patterns obtained by microarrays analysis of brain and lung tumour patients' sera were highly reproducible (R = 0.92-0.96). This provides the technical foundation for diagnostic applications on the basis of auto-antibody patterns. In this limited test set, the assay provided high reproducibility and a broad dynamic range to classify all brain and lung samples correctly. Conclusion Protein microarray is an efficient means for auto-antibody-based detection when using SEREX-derived clones expressing antigenic proteins. Protein microarrays are preferred to macroarrays due to the easier handling and the high reproducibility of auto-antibody testing. Especially when using only a few microliters of patient samples protein microarrays are ideally suited for validation of auto-antibody signatures for diagnostic purposes.
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Affiliation(s)
- René Stempfer
- Molecular Medicine, Austrian Institute of Technology, Seibersdorf, Austria
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Abstract
Aptamers are DNA or RNA oligonucleotides that can bind with high affinity and specificity to a wide range of targets such as proteins, metal ions or pathogenic microorganisms. Soluble aptamers and aptazymes have been used as sensing elements for developing homogeneous assays in a solution phase, the whole sensing process being carried out in a homogeneous solution. Contrary to most conventional heterogeneous assays that are time-consuming and labor-intensive, aptamer-based homogeneous assays are simple, easy-to-perform, rapid and do not require immobilization nor washing steps. To our knowledge, this review is the first entirely dedicated to aptamer-based homogeneous assays. Optical detection appears as the most developed technique. Colorimetry represents the simplest sensing mode that occupies a very important position among aptamer-based assays, involving gold nanoparticle aggregation (with unmodified or aptamer-modified gold NPs), the formation of HRP-mimicking DNAzyme with hemin, dye displacement or interactions with a cationic polymer. Fluorescence that is highly sensitive offers the most developed detection mode. Aptamers can be labeled or not, to give rise to turn-on or usually less sensitive turn-off fluorescent assays. Newly reported and thus less developed non-conventional magnetic resonance imaging (MRI) and electrochemistry also recently appeared in the literature, thrombin still remains the main detected target. Homogeneous assays based on aptazyme, an aptamer sequence connected to a known ribozyme motif, are also described in this review, involving optical detection, by colorimetry or fluorescence.
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Affiliation(s)
- Audrey Sassolas
- CNRS, UMR 5246, ICBMS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Génie Enzymatique, Membranes Biomimétiques et Assemblages Supramoléculaires (GEMBAS), Université Lyon 1, Bât CPE, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622, France
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Lao YH, Peck K, Chen LC. Enhancement of aptamer microarray sensitivity through spacer optimization and avidity effect. Anal Chem 2010; 81:1747-54. [PMID: 19193102 DOI: 10.1021/ac801285a] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This work aims for ultrasensitive detection of target proteins in complex biological matrixes based on aptamer microarrays. Two extensively studied aptamers (HTQ and HTDQ) that bind distinct epitopes of thrombin are chosen for the microarray study. Although HTQ and HTDQ have nanomolar to subnanomolar affinities, it is found that either aptamer when applied directly has difficulty in detecting a few nanomoles per liter thrombin in the presence of a 10- or 100-fold (w/w) excess of serum total protein (STP). By investigating dodecyl (12-carbon) and oligodeoxythymidine (oligo(dT)) spacers, we observe both spacers enhance the microarray signal response, but oligo(dT) is strikingly better than dodecyl. Moreover, we discover that a microarray spot coprinted with the two distinct aptamers (HTQ and HTDQ) functions like a bivalent molecular construct and exhibits an avidity effect. With the synergy of oligo(dT) spacers and the avidity effect, detection of picomolar-range thrombin in the presence of either 10% unlabeled serum or a 10,000-fold excess of labeled serum total protein is achieved. It corresponds to a 100-1000-fold sensitivity enhancement as compared to using an individual aptamer without a spacer.
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Affiliation(s)
- Yeh-Hsing Lao
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
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Han K, Liang Z, Zhou N. Design strategies for aptamer-based biosensors. SENSORS 2010; 10:4541-57. [PMID: 22399891 PMCID: PMC3292130 DOI: 10.3390/s100504541] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/01/2010] [Accepted: 04/04/2010] [Indexed: 11/16/2022]
Abstract
Aptamers have been widely used as recognition elements for biosensor construction, especially in the detection of proteins or small molecule targets, and regarded as promising alternatives for antibodies in bioassay areas. In this review, we present an overview of reported design strategies for the fabrication of biosensors and classify them into four basic modes: target-induced structure switching mode, sandwich or sandwich-like mode, target-induced dissociation/displacement mode and competitive replacement mode. In view of the unprecedented advantages brought about by aptamers and smart design strategies, aptamer-based biosensors are expected to be one of the most promising devices in bioassay related applications.
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Affiliation(s)
- Kun Han
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
- Suzhou Institute of Biomedical Engineering Technology, Chinese Academy of Science, Suzhou 215163, China; E-Mail:
| | - Zhiqiang Liang
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China; E-Mail:
| | - Nandi Zhou
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
- School of Biotechnology and the Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-510-8591-8116; Fax: +86-510-8591-8116
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Tok J, Lai J, Leung T, Li SFY. Molecular aptamer beacon for myotonic dystrophy kinase-related Cdc42-binding kinase alpha. Talanta 2010; 81:732-6. [PMID: 20188990 DOI: 10.1016/j.talanta.2010.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/07/2010] [Accepted: 01/08/2010] [Indexed: 11/18/2022]
Abstract
A novel strategy for the development of molecular aptamer beacon for a signal transduction protein, myotonic dystrophy kinase-related Cdc42-binding kinase (MRCK) was proposed in this work. MRCK is an important downstream effector protein of Cdc42 that phosphorylates proteins involved in organizing actin structures responsible for forming stress fibres, lamellipodia or filopodia. The simple method for MAB design could potentially be applied to other aptamers for modification into a protein probe. The MRCK aptamer was modified into a MAB by adding nucleotides on the 5' end, which are complementary to the 3' end of the aptamer so as to destroy the existing structure and change it into a MB form. In the absence of MRCK, the MAB remained a hairpin structure. However, in the presence of MRCK, the equilibrium was shifted towards the formation of the MRCK-aptamer complex, resulting in the preference for the MRCK-binding conformer, where a fluorescence-quenching pair added to the 5' and 3' ends signaled any protein-dependent conformation change. The development of MABs for signal transduction proteins will have the potential to replace antibodies for diagnostic assays as well as protein studies in cellular imaging.
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Affiliation(s)
- Junie Tok
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Republic of Singapore
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Chiu TC, Huang CC. Aptamer-functionalized nano-biosensors. SENSORS 2009; 9:10356-88. [PMID: 22303178 PMCID: PMC3267226 DOI: 10.3390/s91210356] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 12/12/2022]
Abstract
Nanomaterials have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high surface energy and surface-to-volume ratio, and tunable surface properties. Aptamers are oligonucleotides that can bind their target ligands with high affinity. The use of nanomaterials that are bioconjugated with aptamers for selective and sensitive detection of analytes such as small molecules, metal ions, proteins, and cells has been demonstrated. This review focuses on recent progress in the development of biosensors by integrating functional aptamers with different types of nanomaterials, including quantum dots, magnetic nanoparticles (NPs), metallic NPs, and carbon nanotubes. Colorimetry, fluorescence, electrochemistry, surface plasmon resonance, surface-enhanced Raman scattering, and magnetic resonance imaging are common detection modes for a broad range of analytes with high sensitivity and selectivity when using aptamer bioconjugated nanomaterials (Apt-NMs). We highlight the important roles that the size and concentration of nanomaterials, the secondary structure and density of aptamers, and the multivalent interactions play in determining the specificity and sensitivity of the nanosensors towards analytes. Advantages and disadvantages of the Apt-NMs for bioapplications are focused.
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Affiliation(s)
- Tai-Chia Chiu
- Department of Applied Science, National Taitung University, 684, Section 1, Chunghua Road, Taitung, 95002, Taiwan
- Authors to whom correspondence should be addressed; E-Mails: (T.C.C.); (C.C.H.); Tel.: +886-89-318855 Ext. 3801; Fax: +886-89-342-539
| | - Chih-Ching Huang
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, 2 Beining Road, Keelung, 20224, Taiwan
- Authors to whom correspondence should be addressed; E-Mails: (T.C.C.); (C.C.H.); Tel.: +886-89-318855 Ext. 3801; Fax: +886-89-342-539
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Phillips JA, Xu Y, Xia Z, Fan ZH, Tan W. Enrichment of cancer cells using aptamers immobilized on a microfluidic channel. Anal Chem 2009; 81:1033-9. [PMID: 19115856 DOI: 10.1021/ac802092j] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work describes the development and investigation of an aptamer modified microfluidic device that captures rare cells to achieve a rapid assay without pretreatment of cells. To accomplish this, aptamers are first immobilized on the surface of a poly(dimethylsiloxane) microchannel, followed by pumping a mixture of cells through the device. This process permits the use of optical microscopy to measure the cell-surface density from which we calculate the percentage of cells captured as a function of cell and aptamer concentration, flow velocity, and incubation time. This aptamer-based device was demonstrated to capture target cells with >97% purity and >80% efficiency. Since the cell capture assay is completed within minutes and requires no pretreatment of cells, the device promises to play a key role in the early detection and diagnosis of cancer where rare diseased cells can first be enriched and then captured for detection.
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Affiliation(s)
- Joseph A Phillips
- Center for Research at the Bio/Nano Interface, Department of Chemistry, UF Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
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Wang J, Meng W, Zheng X, Liu S, Li G. Combination of aptamer with gold nanoparticles for electrochemical signal amplification: application to sensitive detection of platelet-derived growth factor. Biosens Bioelectron 2008; 24:1598-602. [PMID: 18829294 DOI: 10.1016/j.bios.2008.08.030] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 07/17/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
Abstract
In this paper, we report a novel electrochemical detection approach for platelet-derived growth factor (PDGF) via "sandwich" structure and gold nanoparticles (Au-NPs) mediated amplification technique. The "sandwich" structure is fabricated based on the fact that PDGF has two aptamer-binding sites, which makes it possible for one PDGF molecule to connect with two aptamers simultaneously. It is found that this electrochemical system with "sandwich" structure and Au-NPs can significantly amplify the signal of electrochemical probe [Ru(NH(3))(5)Cl](2+) for PDGF detection, and thus increase the detection sensitivity significantly. As a result, this PDGF detection approach obtains an extraordinarily low detection limit of 1 x 10(-14)M for purified samples, 1 x 10(-12)M for contaminated-ridden samples or undiluted blood serum. This detection approach can also exhibit good stability and excellent specificity.
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Affiliation(s)
- Jing Wang
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
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Phillips JA, Lopez-Colon D, Zhu Z, Xu Y, Tan W. Applications of aptamers in cancer cell biology. Anal Chim Acta 2008; 621:101-8. [PMID: 18573375 DOI: 10.1016/j.aca.2008.05.031] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/05/2008] [Accepted: 05/06/2008] [Indexed: 01/10/2023]
Abstract
Identifying cells associated with specific disease states is critically important for the early detection and diagnosis of cancer. To facilitate this task, molecular probes, which bind biomarkers that are either specifically or differentially expressed in diseased cells relative to healthy cells, provide a simple and effective method. This review focuses on the use of DNA aptamers as molecular probes for cancer cells. These aptamers are created by means of the cell-based Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, which uses whole disease cells as targets. We describe at length the steps of the cell-SELEX process and discuss several applications for the aptamers, including profiling leukemia patient samples and discovering cell-surface cancer biomarkers. We conclude with a discussion of an aptamer-conjugated nanoparticle enrichment and detection scheme.
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Affiliation(s)
- Joseph A Phillips
- Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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Degefa TH, Kwak J. Label-free aptasensor for platelet-derived growth factor (PDGF) protein. Anal Chim Acta 2008; 613:163-8. [PMID: 18395055 DOI: 10.1016/j.aca.2008.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 03/03/2008] [Accepted: 03/05/2008] [Indexed: 11/19/2022]
Abstract
A label-free aptasensor for platelet-derived growth factor (PDGF) protein is reported. The aptasensor uses mixed self-assembled monolayers (SAMs) composed of a thiol-modified PDGF binding aptamer and 6-mercaptohexanol (MCH) on a gold electrode. The SAMs were characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and differential pulse voltammetry (DPV) before and after binding of the protein using [Fe(CN)(6)](3-/4-), a redox marker ion as an indicator for the formation of a protein-aptamer complex. The CVs at the PDGF modified electrode showed significant differences, such as changes in the peak currents and peak-to-peak separation, before and after binding of the target protein. The EIS spectra, in the form of Nyquist plots, were analyzed with a Randles circuit while the electron transfer resistance R(ct) was used to monitor the binding of the target protein. The results showed that, without any modification to the aptamer, the target protein can be recognized effectively at the PDGF binding aptamer SAMs at the electrode surface. Control experiments using non-binding oligonucleotides assembled at the electrode surfaces also confirmed the results and showed that there was no formation of an aptamer-protein complex. The DPV signal at the aptamer functionalized electrode showed a linearly decreased marker ion peak current in a protein concentrations range of 1-40 nM. Thus, label-free detection of PDGF protein at an aptamer modified electrode has been demonstrated.
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Affiliation(s)
- Tesfaye Hailu Degefa
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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Huang CC, Chiang CK, Lin ZH, Lee KH, Chang HT. Bioconjugated Gold Nanodots and Nanoparticles for Protein Assays Based on Photoluminescence Quenching. Anal Chem 2008; 80:1497-504. [DOI: 10.1021/ac701998f] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chih-Ching Huang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Cheng-Kang Chiang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Zong-Hong Lin
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Kun-Hong Lee
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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Abstract
Real-time monitoring of DNA-protein interactions involving molecular beacon (MB) and molecular beacon aptamer (MBA) was discussed in this chapter. MBs are single-stranded oligonucleotide probes with a hairpin structure. MBs have been designed for oligonucleotide recognition and protein-DNA interaction studies. Real-time monitoring of enzymatic reactions, such as cleavage, ligation, and phosphorylation of single-stranded DNA by specific enzyme, has been studied using MBs. Meanwhile, a new generation of molecular probes, MBA, was designed by combining the excellent signal transduction properties of MBs with the specificity of aptamers for protein recognition. Two different aptamers, the one for thrombin and that for platelet-derived growth factor, have been successfully used to construct MBA probes. The interaction between the proteins and the MBA probes was investigated by fluorescence resonance energy transfer, fluorescence anisotropy, and time-resolved fluorescence. This chapter has reviewed our recent progress in this area.
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Affiliation(s)
- Jun Li
- Department of Chemistry, University of Florida, Gainesville, FL, USA
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Parekh P, Martin J, Chen Y, Colon D, Wang H, Tan W. Using aptamers to study protein-protein interactions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:177-94. [PMID: 18677451 DOI: 10.1007/10_2008_104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The emerging science of systems biology focuses on the systematic study of complex interactions in whole biological systems. A systemic, or integrative, methodology is employed as the chief means of discovering new properties and understanding the aggregate of processes that occur in a biological system. Accordingly, the Human Genome Project has provided a complete map of genes and resultant proteins corresponding to their function. Protein-protein interactions are important pieces of this biological tapestry, and understanding how they work cooperatively in a cell will result in a better understanding of the whole organism. To accomplish this objective, we report the use of DNA/RNA aptamers as a novel tool for the study and elucidation of protein-protein interactions, both in vivo and in vitro.
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Affiliation(s)
- Parag Parekh
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
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Zhou L, Ou LJ, Chu X, Shen GL, Yu RQ. Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. Anal Chem 2007; 79:7492-500. [PMID: 17722881 DOI: 10.1021/ac071059s] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamer-based rolling circle amplification (aptamer-RCA) was developed as a novel versatile electrochemical platform for ultrasensitive detection of protein. This method utilized antibodies immobilized on the electrode surface to capture the protein target, and the surface-captured protein was then sandwiched by an aptamer-primer complex. The aptamer-primer sequence mediated an in situ RCA reaction that generated hundreds of copies of a circular DNA template. Detection of the amplified copies via enzymatic silver deposition then allowed enormous sensitivity enhancement in the assay of target protein. This novel aptamer-primer design circumvented time-consuming preparation of the antibody-DNA conjugate for the common immuno-RCA assay. Moreover, the detection strategy based on enzymatic silver deposition enabled a highly efficient readout of the RCA product as compared to a redox-labeled probe based procedure that might exhibit low detection efficiency due to RCA product distance from the electrode. With the platelet-derived growth factor B-chain (PDGF-BB) as a model target, it was demonstrated that the presented method was highly sensitive and specific with a wide detection range of 4 orders of magnitude and a detection limit as low as 10 fM. Because of the wide availability of aptamers for numerous proteins, this platform holds great promise in ultrasensitive immunoassay.
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Affiliation(s)
- Long Zhou
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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Mairal T, Ozalp VC, Lozano Sánchez P, Mir M, Katakis I, O'Sullivan CK. Aptamers: molecular tools for analytical applications. Anal Bioanal Chem 2007; 390:989-1007. [PMID: 17581746 DOI: 10.1007/s00216-007-1346-4] [Citation(s) in RCA: 382] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 04/30/2007] [Accepted: 05/07/2007] [Indexed: 01/21/2023]
Abstract
Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.
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Affiliation(s)
- Teresa Mairal
- Nanobiotechnology and Bioanalysis Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
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Conley NR, Pomerantz AK, Wang H, Twieg RJ, Moerner WE. Bulk and single-molecule characterization of an improved molecular beacon utilizing H-dimer excitonic behavior. J Phys Chem B 2007; 111:7929-31. [PMID: 17583944 PMCID: PMC2663424 DOI: 10.1021/jp073310d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pairs of fluorophores in close proximity often show self-quenching of fluorescence by the well-known H-dimer mechanism. We use a pair of fluorophores in the new dicyanomethylenedihydrofuran (DCDHF) dye family in the design and characterization of a new fluorescent probe for nucleic acid detection, which we refer to as a self-quenched intramolecular dimer (SQuID) molecular beacon (MB). We obtain a quenching efficiency of 97.2%, higher than the only other reported value for a MB employing fluorophore self-quenching by H-dimer formation. Furthermore, the excellent single-molecule (SM) emitter characteristics of the DCDHF dyes allow observation of individual SQuID MB-target complexes immobilized on a surface, where the doubled SM emission intensity of our target-bound beacon ensures a higher signal-to-background ratio than conventional fluorophore-quencher MBs. Additional advantages of the SQuID MB are single-pot labeling, visible colorimetric detection of the target, and intrinsic single-molecule two-step photobleaching behavior, which offers a specific means of discriminating between functional MBs and spurious fluorescence.
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Polsky R, Gill R, Kaganovsky L, Willner I. Nucleic acid-functionalized Pt nanoparticles: Catalytic labels for the amplified electrochemical detection of biomolecules. Anal Chem 2007; 78:2268-71. [PMID: 16579607 DOI: 10.1021/ac0519864] [Citation(s) in RCA: 340] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid-functionalized Pt nanoparticles (Pt-NPs) act as catalytic labels for the amplified electrochemical detection of DNA hybridization and aptamer/protein recognition. Hybridization of the nucleic acid-modified Pt-NPs with a sensing nucleic acid/analyte DNA complex associated with an electrode enables the amperometric, amplified, detection of the DNA by the Pt NP electrocatalyzed reduction of H2O2 (sensitivity limit, 1 x 10(-11) M). Similarly, the association of aptamer-functionalized Pt- NPs to a thrombin aptamer/thrombin complex associated with an electrode allowed the amplified, electrocatalytic detection of thrombin with a sensitivity limit corresponding to 1 x 10(-9) M.
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Affiliation(s)
- Ronen Polsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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