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Settu K, Liu JT, Chen CJ, Tsai JZ. Development of carbon-graphene-based aptamer biosensor for EN2 protein detection. Anal Biochem 2017; 534:99-107. [PMID: 28709900 DOI: 10.1016/j.ab.2017.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/01/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022]
Abstract
In this study, we developed a screen-printed carbon-graphene-based electrochemical biosensor for EN2 protein detection. The engrailed-2 (EN2) protein, a biomarker for prostate cancer, is known to be a strong binder to a specific DNA sequence (5'-TAATTA-3') to regulate transcription. To take advantage of this intrinsic property, aptamer probes with TAATTA sequence was immobilized onto the screen-printed carbon-graphene electrode surface via EDC-NHS coupling approach. Cyclic voltammetry (CV) of the electrochemical measurement technique was employed for the quantitative detection of EN2 protein. The hindrance to the redox reaction of potassium ferricyanide on the biosensor surface due to the binding of the immobilized aptamer with its target EN2 protein quantified the protein concentration. Under optimum conditions, the aptamer biosensor can detect EN2 protein over a linear range from 35 to 185 nM with a detection limit of 38.5 nM.
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Affiliation(s)
- Kalpana Settu
- Department of Electrical Engineering, National Taipei University, Sanxia, Taiwan
| | - Jen-Tsai Liu
- College of Materials Sciences and Opto-electronics, University of Chinese Academy of Sciences, Beijing, China
| | - Ching-Jung Chen
- School of Electronic and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Jang-Zern Tsai
- Department of Electrical Engineering, National Central University, Jhongli, Taiwan.
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102
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Wang J, Gu Y, Liu L, Wang C, Wang J, Ding S, Li J, Qiu L, Jiang P. Novel application of fluorescence coupled capillary electrophoresis to resolve the interaction between the G-quadruplex aptamer and thrombin. J Sep Sci 2017; 40:3161-3167. [PMID: 28594110 DOI: 10.1002/jssc.201700456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/27/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022]
Abstract
The dynamic binding status between the thrombin and its G-quadruplex aptamers and the stability of its interaction partners were probed using our previously established fluorescence-coupled capillary electrophoresis method. A 29-nucleic acid thrombin binding aptamer was chosen as a model to study its binding affinity with the thrombin ligand. First, the effects of the cations on the formation of G-quadruplex from unstructured 29-nucleic acid thrombin binding aptamer were examined. Second, the rapid binding kinetics between the thrombin and 6-carboxyfluorescein labeled G-quadruplex aptamer was measured. Third, the stability of G-quadruplex aptamer-thrombin complex was also examined in the presence of the interfering species. Remarkably, it was found that the complementary strand of 29-nucleic acid thrombin binding aptamer could compete with G-quadruplex aptamer and thus disassociated the G-quadruplex structure into an unstructured aptamer. These data suggest that our in-house established fluorescence-coupled capillary electrophoresis assay could be applied to binding studies of the G-quadruplex aptamers, thrombin, and their ligands, while overcoming the complicated and costly approaches currently available.
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Affiliation(s)
- Jianhao Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Yaqin Gu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Li Liu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Cheli Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Jianpeng Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Shumin Ding
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Jinping Li
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China.,Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA, USA
| | - Lin Qiu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Pengju Jiang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
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103
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El-Samadony H, Althani A, Tageldin MA, Azzazy HME. Nanodiagnostics for tuberculosis detection. Expert Rev Mol Diagn 2017; 17:427-443. [PMID: 28317400 DOI: 10.1080/14737159.2017.1308825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is a leading killer worldwide. End TB strategy aims at ending the TB epidemic by 2030. Early, accurate, and affordable diagnosis represents a cornerstone to achieve this goal. Innovative strategies for TB diagnostics have been introduced. However, the ideal assay is yet unavailable and conventional methods remain necessary for diagnosis. Unique properties of nanoparticles (NPs) have allowed their utilization in TB detection via targeting disease biomarkers. Area covered: Until now, around thirty-five TB NP-based assays have been partially or fully characterized. Accuracy, low-cost, and short time-to-result represent the common properties of proposed platforms. TB nanodiagnostics now encompass almost all clinical aspects of the disease including active TB, non-tuberculous mycobacteria, rifampicin resistant TB, TB/HIV co-infection, latent TB, and extra-pulmonary TB. This review summarizes state-of-the-art knowledge of TB nanodiagnostics for the last 10 years. Special consideration is given for fabrication concepts, detection strategies, and clinical performance using various clinical specimens. The potential of TB nanodiagnostics to fulfill the need for ideal MTB testing is assessed. Expert commentary: TB nanodiagnostics show promise to be ideal detection tools that can meet the rigorous demands to end the TB epidemic by 2030.
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Affiliation(s)
| | - Asma Althani
- b Health Sciences Department, College of Arts and Sciences , Qatar University , Doha , Qatar
| | - Mohamed Awad Tageldin
- c Department of Chest Diseases, Faculty of Medicine , Ain Shams University , Cairo , Egypt
| | - Hassan M E Azzazy
- d Department of Chemistry, School of Sciences & Engineering , the American University in Cairo , New Cairo , Egypt
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104
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Luby BM, Charron DM, MacLaughlin CM, Zheng G. Activatable fluorescence: From small molecule to nanoparticle. Adv Drug Deliv Rev 2017; 113:97-121. [PMID: 27593264 DOI: 10.1016/j.addr.2016.08.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/15/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
Molecular imaging has emerged as an indispensable technology in the development and application of drug delivery systems. Targeted imaging agents report the presence of biomolecules, including therapeutic targets and disease biomarkers, while the biological behaviour of labelled delivery systems can be non-invasively assessed in real time. As an imaging modality, fluorescence offers additional signal specificity and dynamic information due to the inherent responsivity of fluorescence agents to interactions with other optical species and with their environment. Harnessing this responsivity is the basis of activatable fluorescence imaging, where interactions between an engineered fluorescence agent and its biological target induce a fluorogenic response. Small molecule activatable agents are frequently derivatives of common fluorophores designed to chemically react with their target. Macromolecular scale agents are useful for imaging proteins and nucleic acids, although their biological delivery can be difficult. Nanoscale activatable agents combine the responsivity of fluorophores with the unique optical and physical properties of nanomaterials. The molecular imaging application and overall complexity of biological target dictate the most advantageous fluorescence agent size scale and activation strategy.
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Affiliation(s)
- Benjamin M Luby
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Danielle M Charron
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Christina M MacLaughlin
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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105
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Lv X, Zhang Y, Liu G, Du L, Wang S. Aptamer-based fluorescent detection of ochratoxin A by quenching of gold nanoparticles. RSC Adv 2017. [DOI: 10.1039/c7ra01474k] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A simple, rapid, low cost and highly sensitive method for the detection of ochratoxin A (OTA) was developed based on the principle that dispersed AuNPs show a better fluorescence quenching effect than aggregated AuNPs.
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Affiliation(s)
- Xin Lv
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Yuanfu Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Guofu Liu
- College of Life Science
- Liaocheng University
- Liaocheng 252059
- China
| | - Lingyun Du
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Shuhao Wang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
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106
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Jeong JE, Woo HY. Control of electrostatic interaction between a molecular beacon aptamer and conjugated polyelectrolyte for detection range-tunable ATP assay. Polym Chem 2017. [DOI: 10.1039/c7py01252g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new strategy is suggested to fine-tune the detection range by controlling the ionic density of CPEs in the MBA/CPE-based ATP assay.
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Affiliation(s)
- J.-E. Jeong
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
| | - H. Y. Woo
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
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107
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Kim J, Kim D, Lee JB. DNA aptamer-based carrier for loading proteins and enhancing the enzymatic activity. RSC Adv 2017. [DOI: 10.1039/c6ra25507h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here, we synthesized DNA microparticles comprised of thrombin binding aptamers via rolling circle amplification (RCA). These DNA aptamer particles could successfully load a number of thrombins and the complexes have shown improved thrombin activity.
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Affiliation(s)
- Jieun Kim
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
| | - Dajeong Kim
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
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108
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Hwang J, Seo Y, Jo Y, Son J, Choi J. Aptamer-conjugated live human immune cell based biosensors for the accurate detection of C-reactive protein. Sci Rep 2016; 6:34778. [PMID: 27708384 PMCID: PMC5052522 DOI: 10.1038/srep34778] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/19/2016] [Indexed: 01/27/2023] Open
Abstract
C-reactive protein (CRP) is a pentameric protein that is present in the bloodstream during inflammatory events, e.g., liver failure, leukemia, and/or bacterial infection. The level of CRP indicates the progress and prognosis of certain diseases; it is therefore necessary to measure CRP levels in the blood accurately. The normal concentration of CRP is reported to be 1–3 mg/L. Inflammatory events increase the level of CRP by up to 500 times; accordingly, CRP is a biomarker of acute inflammatory disease. In this study, we demonstrated the preparation of DNA aptamer-conjugated peripheral blood mononuclear cells (Apt-PBMCs) that specifically capture human CRP. Live PBMCs functionalized with aptamers could detect different levels of human CRP by producing immune complexes with reporter antibody. The binding behavior of Apt-PBMCs toward highly concentrated CRP sites was also investigated. The immune responses of Apt-PBMCs were evaluated by measuring TNF-alpha secretion after stimulating the PBMCs with lipopolysaccharides. In summary, engineered Apt-PBMCs have potential applications as live cell based biosensors and for in vitro tracing of CRP secretion sites.
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Affiliation(s)
- Jangsun Hwang
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Youngmin Seo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeonho Jo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaewoo Son
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jonghoon Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
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109
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Xu W, Tian J, Shao X, Zhu L, Huang K, Luo Y. A rapid and visual aptasensor for Lipopolysaccharides detection based on the bulb-like triplex turn-on switch coupled with HCR-HRP nanostructures. Biosens Bioelectron 2016; 89:795-801. [PMID: 27816585 DOI: 10.1016/j.bios.2016.10.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/24/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
Abstract
For previously reported aptasensor, the sensitivity and selectivity of aptamers to targets were often suppressed due to the reporter label of single-stranded molecular beacon or hindrance of the duplex DNA strand displacement. To solve the affinity declining of aptamers showed in traditional way and realize on-site rapid detection of Lipopolysaccharides (LPS), we developed an ingenious structure-switching aptasensor based on the bulb-like triplex turn-on switch (BTTS) as the effective molecular recognition and signal transduction element and streptavidin-horseradish peroxidase modified hybridization chain reaction (HCR-HRP) nanocomposites as the signal amplifier and signal report element. In the presence of LPS, the bulb-like LPS-aptamer (BLA) and LPS formed the LPS/aptamer complex, while the BTTS disassembled and liberated the dissociative bridge probes (BP) to achieve molecular recognition and signal transduction. Immobilized BP, captured by immobilized capture probes (CP), triggered hybridization chain reactions (HCR) to amplify the switching signal, and the HCR products were then modified with streptavidin-horseradish peroxidase (SA-HRP) to form HCR-HRP nanostructures to output colorimetric signals. In less than four hours, the proposed biosensor showed a detection limit of 50pg/mL of LPS quantitatively with the portable spectrophotometer and the observation limit of 20ng/mL semi-quantitatively with the naked eye, opening up new opportunities for LPS detection in future clinical diagnosis, food security and environment monitoring.
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Affiliation(s)
- Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingjing Tian
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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110
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A simple and label-free aptasensor based on amino group-functionalized gold nanocomposites-Prussian blue/carbon nanotubes as labels for signal amplification. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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111
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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112
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Azadbakht A, Roushani M, Abbasi AR, Menati S, Derikvand Z. A label-free aptasensor based on polyethyleneimine wrapped carbon nanotubes in situ formed gold nanoparticles as signal probe for highly sensitive detection of dopamine. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 68:585-593. [PMID: 27524058 DOI: 10.1016/j.msec.2016.05.077] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/10/2016] [Accepted: 05/18/2016] [Indexed: 11/27/2022]
Abstract
Herein, a highly sensitive and selective aptamer biosensor for quantitative detection of a model target, dopamine (DA), was developed by using a gold (Au) electrode modified with highly dispersed gold nanoparticles (AuNPs) and acid-oxidized carbon nanotubes (CNTs-COOH) functionalized with polyethyleneimine (PEI). Amine-terminated12-mercaptureprobe (ssDNA1) as a capture probe and specific DA-aptamer (ssDNA2) as a detection probe was immobilized on the surface of a modified electrode via the formation of covalent amide bond and hybridization, respectively. Methylene blue (MB) was used as the redox probe, which was intercalated into the aptamer through the specific interaction with its guanine bases. In the presence of DA, the interaction between aptamer and DA displaced the MB from the electrode surface, rendering a lowered electrochemical signal attributed to decreased amount of adsorbed MB. The developed electrochemical DA aptasensor showed a good linear response to DA from 5 to 300nM with detection limit of 2.1nM. The biosensor also exhibited satisfactory selectivity and could be successfully used to detect DA in blood serum sample.
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Affiliation(s)
- Azadeh Azadbakht
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran.
| | | | - Amir Reza Abbasi
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Saeid Menati
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Zohreh Derikvand
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
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113
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Affiliation(s)
- Dae-Ro Ahn
- Life Sciences Research Division, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, South Korea
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114
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Wu YX, Kwon YJ. Aptamers: The "evolution" of SELEX. Methods 2016; 106:21-8. [PMID: 27109056 DOI: 10.1016/j.ymeth.2016.04.020] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/09/2023] Open
Abstract
It has been more than two decades since the first aptamer molecule was discovered. Since then, aptamer molecules have gain much attention in the scientific field. This increasing traction can be attributed to their many desirable traits, such as 1) their potentials to bind a wide range of molecules, 2) their malleability, and 3) their low cost of production. These traits have made aptamer molecules an ideal platform to pursue in the realm of pharmaceuticals and bio-sensors. Despite the broad applications of aptamers, tedious procedure, high resource consumption, and limited nucleobase repertoire have hindered aptamer in application usage. To address these issues, new innovative methodologies, such as automation and single round SELEX, are being developed to improve the outcomes and rates in which aptamers are discovered.
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Affiliation(s)
- Yi Xi Wu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States; Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States; Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States.
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115
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Lin S, Gan N, Cao Y, Chen Y, Jiang Q. Selective dispersive solid phase extraction-chromatography tandem mass spectrometry based on aptamer-functionalized UiO-66-NH2 for determination of polychlorinated biphenyls. J Chromatogr A 2016; 1446:34-40. [PMID: 27083256 DOI: 10.1016/j.chroma.2016.04.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
In this paper, a novel dispersive solid phase extraction (dSPE) adsorbent based on aptamer-functionalized magnetic metal-organic framework material was developed for selective enrichment of the trace polychlorinated biphenyls (PCBs) from soil sample. Firstly, we developed a simple, versatile synthetic strategy to prepare highly reproducible magnetic amino-functionalized UiO-66 (Fe3O4@PDA@UiO-66-NH2) by using polydopamine (PDA) as covalent linker. Then amino-functionalized aptamers which can recognize 2,3',5,5'-tetrachlorobiphenyl (PCB72), 2',3',4',5,5'-pentachlorobiphenyl (PCB106) were covalent immobilized on UiO-66-NH2 through coupling reagent of glutaraldehyde. Aptamer-functionalized adsorbent (Fe3O4@PDA@UiO-66-Apt) can specifically capture PCBs from complex matrix with high adsorption capacity based on the specific affinity of aptamer towards target. Moreover, the adsorbent can be easily isolated from the solution through magnetic separation after extraction. Afterwards, the detection was carried out with gas chromatography tandem mass spectrometry (GC-MS). The selective dSPE pretreatment coupled with GC-MS possessed high selectivity, good binding capacity, stability, repeatability and reproducibility for the extraction of PCBs. Furthermore, the adsorbent possessed good mechanical stability which can be applied in replicate at least for 60 extraction cycles with recovery over 80%. It provided a linear range of 0.02-400ngmL(-1) with a good correlation coefficient (R(2)=0.9994-0.9996), and the limit of detection was found to be 0.010-0.015ngmL(-1). The method was successfully utilized for the determination of PCBs in soil samples.
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Affiliation(s)
- Saichai Lin
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Ning Gan
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yuting Cao
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Yinji Chen
- Deptartment of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210007, China
| | - Qianli Jiang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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116
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Selective amyloid β oligomer assay based on abasic site-containing molecular beacon and enzyme-free amplification. Biosens Bioelectron 2016; 78:206-212. [DOI: 10.1016/j.bios.2015.11.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/31/2015] [Accepted: 11/15/2015] [Indexed: 12/21/2022]
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117
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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Construction of Au-IDE/CFP10-ESAT6 aptamer/DNA-AuNPs MSPQC for rapid detection of Mycobacterium tuberculosis. Biosens Bioelectron 2016; 77:799-804. [DOI: 10.1016/j.bios.2015.10.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 11/22/2022]
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Ranjbar R, Hafezi-Moghadam MS. Design and construction of a DNA origami drug delivery system based on MPT64 antibody aptamer for tuberculosis treatment. Electron Physician 2016; 8:1857-64. [PMID: 27053991 PMCID: PMC4821297 DOI: 10.19082/1857] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/24/2015] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION With all of the developments on infectious diseases, tuberculosis (TB) remains a cause of death among people. One of the most promising assembly techniques in nano-technology is "scaffolded DNA origami" to design and construct a nano-scale drug delivery system. Because of the global health problems of tuberculosis, the development of potent new anti-tuberculosis drug delivery system without cross-resistance with known anti-mycobacterial agents is urgently needed. The aim of this study was to design a nano-scale drug delivery system for TB treatment using the DNA origami method. METHODS In this study, we presented an experimental research on a DNA drug delivery system for treating Tuberculosis. TEM images were visualized with an FEI Tecnai T12 BioTWIN at 120 kV. The model was designed by caDNAno software and computational prediction of the 3D solution shape and its flexibility was calculated with a CanDo server. RESULTS Synthesizing the product was imaged using transmission electron microscopy after negative-staining by uranyl formate. CONCLUSION We constructed a multilayer 3D DNA nanostructure system by designing square lattice geometry with the scaffolded-DNA-origami method. With changes in the lock and key sequences, we recommend that this system be used for other infectious diseases to target the pathogenic bacteria.
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Affiliation(s)
- Reza Ranjbar
- Ph.D., Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Chattaraj R, Mohan P, Livingston CM, Besmer JD, Kumar K, Goodwin AP. Mutually-Reactive, Fluorogenic Hydrocyanine/Quinone Reporter Pairs for In-Solution Biosensing via Nanodroplet Association. ACS APPLIED MATERIALS & INTERFACES 2016; 8:802-8. [PMID: 26710239 PMCID: PMC5051691 DOI: 10.1021/acsami.5b10036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mutually reactive, fluorogenic molecules are presented as a simple and novel technique for in-solution biosensing. The hypothesis behind this work was that aggregating droplets into close proximity would cause rapid mixing of their contents. To take advantage of this effect, a novel pair of fluorogenic redox molecules were designed to remain in lipid-stabilized oil droplets but mix once aggregated. First, the hydrophobic cyanine dye 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) was reduced with sodium borohydride to form a nonfluorescent analog (HDiI). Hydrophobic quinone derivatives were then screened as oxidizing agents, and it was found that p-fluoranil oxidized nonfluorescent HDiI back to fluorescent DiI. Next, HDiI and p-fluoranil were loaded into NEOBEE oil nanodroplets of average diameter 600 nm that were stabilized by a monolayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE)-polyethylene glycol (PEG), and DSPE-PEG-biotin. Addition of streptavidin caused aggregation of droplets and the appearance of red fluorescent aggregates within 30 min. Next, Nanoparticle Tracking Analysis was used to record the fluorescence of the droplets and their aggregates. By integrating the fluorescence emission of the tracked droplets, streptavidin could be detected down to 100 fM. Finally, the droplets were reformulated to sense for vascular endothelial growth factor (VEGF), a biomarker for tumor metastasis. Using anti-VEGF aptamers attached to DSPE-PEG incorporated into the nanodroplet monolayer, VEGF could also be detected down to 100 fM.
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Affiliation(s)
- Rajarshi Chattaraj
- Department of Mechanical Engineering, University of Colorado Boulder. Boulder, CO 80309
| | - Praveena Mohan
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Clare M. Livingston
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Jeremy D. Besmer
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Kaushlendra Kumar
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Andrew P. Goodwin
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
- Corresponding Author: To whom correspondence should be addressed:
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122
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Ma F, Zhang CY. Histone modifying enzymes: novel disease biomarkers and assay development. Expert Rev Mol Diagn 2016; 16:297-306. [DOI: 10.1586/14737159.2016.1135057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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123
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Lv Y, Wu J, Wu P, Chen YZ, Tan Y, Tan C, Jiang Y. A sensitive polymeric dark quencher-based sensing platform for fluorescence “turn on” detection of proteins. RSC Adv 2016. [DOI: 10.1039/c6ra07310g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A sensing platform consisting of polymeric dark quenchers and oppositely charged probes was constructed for detection of proteins.
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Affiliation(s)
- Ying Lv
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Jiatao Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Pan Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yu Zong Chen
- Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics
- Shenzhen Kivita Innovative Drug Discovery Institute
- Shenzhen 518055
- P. R. China
| | - Ying Tan
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
| | - Chunyan Tan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
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Mahmood MAI, Hasan MR, Khan UJM, Allen PB, Kim YT, Ellington AD, Iqbal SM. One-step tumor detection from dynamic morphology tracking on aptamer-grafted surfaces. TECHNOLOGY 2015; 3:194-200. [PMID: 26753172 PMCID: PMC4703374 DOI: 10.1142/s2339547815500089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this paper, we report a one-step tumor cell detection approach based on the dynamic morphological behavior tracking of cancer cells on a ligand modified surface. Every cell on the surface was tracked in real time for several minutes immediately after seeding until these were finally attached. Cancer cells were found to be very active in the aptamer microenvironment, changing their shapes rapidly from spherical to semi-elliptical, with much flatter spread and extending pseudopods at regular intervals. When incubated on a functionalized surface, the balancing forces between cell surface molecules and the surface-bound aptamers, together with the flexibility of the membranes, caused cells to show these distinct dynamic activities and variations in their morphologies. On the other hand, healthy cells remained distinguishingly inactive on the surface over the same period. The quantitative image analysis of cell morphologies provided feature vectors that were statistically distinct between normal and cancer cells.
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Affiliation(s)
- Mohammed Arif I Mahmood
- Nano-Bio Lab, University of Texas at Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas at Arlington, TX 76010, USA; Nanotechnology Research Center, University of Texas at Arlington, TX 76019, USA
| | - Mohammad Raziul Hasan
- Nano-Bio Lab, University of Texas at Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas at Arlington, TX 76010, USA; Nanotechnology Research Center, University of Texas at Arlington, TX 76019, USA
| | - Umair J M Khan
- Nano-Bio Lab, University of Texas at Arlington, TX 76019, USA; Nanotechnology Research Center, University of Texas at Arlington, TX 76019, USA; Department of Biology, University of Texas at Arlington, TX 76019, USA
| | - Peter B Allen
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Now at Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA
| | - Young-Tae Kim
- Nanotechnology Research Center, University of Texas at Arlington, TX 76019, USA; Department of Bioengineering, University of Texas at Arlington, TX 76011, USA; Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Andrew D Ellington
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Samir M Iqbal
- Nano-Bio Lab, University of Texas at Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas at Arlington, TX 76010, USA; Nanotechnology Research Center, University of Texas at Arlington, TX 76019, USA; Department of Biology, University of Texas at Arlington, TX 76019, USA; Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
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Xing XJ, Xiao WL, Liu XG, Zhou Y, Pang DW, Tang HW. A fluorescent aptasensor using double-stranded DNA/graphene oxide as the indicator probe. Biosens Bioelectron 2015; 78:431-437. [PMID: 26655184 DOI: 10.1016/j.bios.2015.11.076] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 01/09/2023]
Abstract
We developed a fluorescent aptasensor based on the making use of double-stranded DNA (dsDNA)/graphene oxide (GO) as the signal probe and the activities of exonuclease I (Exo I). This method takes advantage of the stronger affinity of the aptamer to its target rather than to its complementary sequence (competitor), and the different interaction intensity of dsDNA, mononucleotides with GO. Specifically, in the absence of target, the competitor hybridizes with the aptamer, preventing the digestion of the competitor by Exo I, and thus the formed dsDNA is adsorbed on GO surface, allowing fluorescence quenching. When the target is introduced, the aptamer preferentially binds with its target. Thereby, the corresponding nuclease reaction takes place, and slight fluorescence change is obtained after the introduction of GO due to the weak affinity of the generated mononucleotides to GO. Adenosine (AD) was chosen as a model system and tested in detail. Under the optimized conditions, smaller dissociation constant (Kd, 311.0 µM) and lower detection limit (LOD, 3.1 µM) were obtained in contrast with traditional dye-labeled aptamer/GO based platform (Kd=688.8 µM, LOD=21.2 µM). Satisfying results were still obtained in the evaluation of the specificity and the detection of AD in human serum, making it a promising tool for the diagnosis of AD-relevant diseases. Moreover, we demonstrated the effect of the competitor on the LOD, and the results reveal that the sensitivity could be enhanced by using the rational competitor. The present design not only constructs a label-free aptamer based platform but also extends the application of dsDNA/GO complex in biochemical and biomedical studies.
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Affiliation(s)
- Xiao-Jing Xing
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, Wuhan University, Wuhan 430072, China; College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Wan-Lu Xiao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, Wuhan University, Wuhan 430072, China
| | - Xue-Guo Liu
- Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang 473004, China
| | - Ying Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, Wuhan University, Wuhan 430072, China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, Wuhan University, Wuhan 430072, China
| | - Hong-Wu Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, Wuhan University, Wuhan 430072, China.
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Lin S, Gan N, Zhang J, Qiao L, Chen Y, Cao Y. Aptamer-functionalized stir bar sorptive extraction coupled with gas chromatography-mass spectrometry for selective enrichment and determination of polychlorinated biphenyls in fish samples. Talanta 2015; 149:266-274. [PMID: 26717840 DOI: 10.1016/j.talanta.2015.11.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
In this paper, a novel aptamer-functionalized stir bar sorptive extraction (SBSE) was developed for selective enrichment of the low abundance polychlorinated biphenyls (PCBs) from fish samples. This approach was based on the immobilization of aptamer which could recognize 2,3',5,5'-tetrachlorobiphenyl (PCB72) and 2',3',4',5,5'-pentachlorobiphenyl (PCB106) on one kind of metal-organic frameworks (Zn4O(BDC)3, MOF-5). MOF-5 as a substrate was prepared by potential-controlled cathodic electrodeposition on stainless steel. This aptamer-functionalized stir bar sorptive extraction (Apt-MOF SBSE) fiber could be facile synthesized in one-step. PCB72 and PCB106 were employed as target analytes for selective extraction by the developed method. The adsorbed targets could be desorbed easily in pH 3.0 100mM glycine-HCl buffers and then extracted by the methylene chloride. Afterwards, the detection was carried out with gas chromatography-tandem mass spectrometry (GC-MS). The Apt-MOF SBSE pretreatment coupled with GC-MS exhibited high selectivity, good binding capacity, stability and reproducibility for the detection of PCBs. It provided a linear range of 0.02-250ngmL(-1) with a good coefficient of determination (R(2)=0.9991-0.9996) and the detection limit was 0.003-0.004ngmL(-1). More importantly, the method was successfully utilized for the determination of PCBs in fish samples with good enrichment factor (1930-2304). Therefore, this new SBSE coating opens up the possibility of selective enrichment of a given target PCBs from complex fish samples.
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Affiliation(s)
- Saichai Lin
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Ning Gan
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Jiabin Zhang
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Li Qiao
- Faculty of Marine Science, Ningbo University, Ningbo 315211, China
| | - Yinji Chen
- Deptartment of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance & Economics, Nanjing, China
| | - Yuting Cao
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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Mukherjee S, Meshik X, Choi M, Farid S, Datta D, Lan Y, Poduri S, Sarkar K, Baterdene U, Huang CE, Wang YY, Burke P, Dutta M, Stroscio MA. A Graphene and Aptamer Based Liquid Gated FET-Like Electrochemical Biosensor to Detect Adenosine Triphosphate. IEEE Trans Nanobioscience 2015; 14:967-72. [PMID: 26595926 DOI: 10.1109/tnb.2015.2501364] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Here we report successful demonstration of a FET-like electrochemical nano-biosensor to accurately detect ultralow concentrations of adenosine triphosphate. As a 2D material, graphene is a promising candidate due to its large surface area, biocompatibility, and demonstrated surface binding chemistries and has been employed as the conducting channel. A short 20-base DNA aptamer is used as the sensing element to ensure that the interaction between the analyte and the aptamer occurs within the Debye length of the electrolyte (PBS). Significant increase in the drain current with progressive addition of ATP is observed whereas for control experiments, no distinct change in the drain current occurs. The sensor is found to be highly sensitive in the nanomolar (nM) to micromolar ( μM) range with a high sensitivity of 2.55 μA (mM) (-1), a detection limit as low as 10 pM, and it has potential application in medical and biological settings to detect low traces of ATP. This simplistic design strategy can be further extended to efficiently detect a broad range of other target analytes.
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128
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Highly Sensitive Fluorescent Aptasensor for Thrombin Detection Based on Competition Triggered Rolling Circle Amplification. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60880-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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129
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Yan M, Bai W, Zhu C, Huang Y, Yan J, Chen A. Design of nuclease-based target recycling signal amplification in aptasensors. Biosens Bioelectron 2015; 77:613-23. [PMID: 26485175 DOI: 10.1016/j.bios.2015.10.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Compared with conventional antibody-based immunoassay methods, aptasensors based on nucleic acid aptamer have made at least two significant breakthroughs. One is that aptamers are more easily used for developing various simple and rapid homogeneous detection methods by "sample in signal out" without multi-step washing. The other is that aptamers are more easily employed for developing highly sensitive detection methods by using various nucleic acid-based signal amplification approaches. As many substances playing regulatory roles in physiology or pathology exist at an extremely low concentration and many chemical contaminants occur in trace amounts in food or environment, aptasensors for signal amplification contribute greatly to detection of such targets. Among the signal amplification approaches in highly sensitive aptasensors, the nuclease-based target recycling signal amplification has recently become a research focus because it shows easy design, simple operation, and rapid reaction and can be easily developed for homogenous assay. In this review, we summarized recent advances in the development of various nuclease-based target recycling signal amplification with the aim to provide a general guide for the design of aptamer-based ultrasensitive biosensing assays.
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Affiliation(s)
- Mengmeng Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Chao Zhu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Yafei Huang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Jiao Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
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130
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Yang D, Ning L, Gao T, Ye Z, Li G. Enzyme-free dual amplification strategy for protein assay by coupling toehold-mediated DNA strand displacement reaction with hybridization chain reaction. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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131
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Abstract
Biosensors first appeared several decades ago to address the need for monitoring physiological parameters such as oxygen or glucose in biological fluids such as blood. More recently, a new wave of biosensors has emerged in order to provide more nuanced and granular information about the composition and function of living cells. Such biosensors exist at the confluence of technology and medicine and often strive to connect cell phenotype or function to physiological or pathophysiological processes. Our review aims to describe some of the key technological aspects of biosensors being developed for cell analysis. The technological aspects covered in our review include biorecognition elements used for biosensor construction, methods for integrating cells with biosensors, approaches to single-cell analysis, and the use of nanostructured biosensors for cell analysis. Our hope is that the spectrum of possibilities for cell analysis described in this review may pique the interest of biomedical scientists and engineers and may spur new collaborations in the area of using biosensors for cell analysis.
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Affiliation(s)
- Qing Zhou
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Kyungjin Son
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Ying Liu
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis, California 95616;
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132
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Zhu B, Booth MA, Woo HY, Hodgkiss JM, Travas-Sejdic J. Label-Free, Electrochemical Quantitation of Potassium Ions from Femtomolar Levels. Chem Asian J 2015; 10:2169-75. [DOI: 10.1002/asia.201500313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/29/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bicheng Zhu
- School of Chemical Sciences; Polymer Electronics Research Centre (PERC); The University of Auckland; 23 Symonds Street Auckland New Zealand
| | - Marsilea A. Booth
- Digital Sensing Limited; 16 Beatrice Tinsley Cresent, Albany Auckland 0632 New Zealand
| | - Han Young Woo
- Department of Cogno Mechatronics Engineering; Pusan National University; Miryang 627-706 Republic of Korea
| | - Justin M. Hodgkiss
- The MacDiarmid Institute for Advanced Materials and Nanotechnology; Laby 410, Gate 6 Kelburn Parade Kelburn, Wellington New Zealand
- School of Chemical and Physical Sciences; Victoria University of Wellington; Wellington New Zealand
| | - Jadranka Travas-Sejdic
- School of Chemical Sciences; Polymer Electronics Research Centre (PERC); The University of Auckland; 23 Symonds Street Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology; Laby 410, Gate 6 Kelburn Parade Kelburn, Wellington New Zealand
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Urmann K, Tenenbaum E, Walter JG, Segal E. Porous Silicon Biosensors Employing Emerging Capture Probes. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20346-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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134
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Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing. SENSORS 2015; 15:16281-313. [PMID: 26153774 PMCID: PMC4541879 DOI: 10.3390/s150716281] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 02/06/2023]
Abstract
Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed.
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135
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A Microfluidic Love-Wave Biosensing Device for PSA Detection Based on an Aptamer Beacon Probe. SENSORS 2015; 15:13839-50. [PMID: 26110408 PMCID: PMC4507688 DOI: 10.3390/s150613839] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
Abstract
A label-free and selective aptamer beacon-based Love-wave biosensing device was developed for prostate specific antigen (PSA) detection. The device consists of the following parts: LiTaO3 substrate with SiO2 film as wave guide layer, two set of inter-digital transducers (IDT), gold film for immobilization of the biorecongniton layer and a polydimethylsiloxane (PDMS) microfluidic channels. DNA aptamer, or “artificial antibody”, was used as the specific biorecognition probe for PSA capture. Some nucleotides were added to the 3'-end of the aptamer to form a duplex with the 3'-end, turning the aptamer into an aptamer-beacon. Taking advantage of the selective target-induced assembly changes arising from the “aptamer beacon”, highly selective and specific detection of PSA was achieved. Furthermore, PDMS microfluidic channels were designed and fabricated to realize automated quantitative sample injection. After optimization of the experimental conditions, the established device showed good performance for PSA detection between 10 ng/mL to 1 μg/mL, with a detection limit of 10 ng/mL. The proposed sensor might be a promising alternative for point of care diagnostics.
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136
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Yin J, Zhang A, Dong C, Ren J. An aptamer-based single particle method for sensitive detection of thrombin using fluorescent quantum dots as labeling probes. Talanta 2015; 144:13-9. [PMID: 26452786 DOI: 10.1016/j.talanta.2015.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 01/28/2023]
Abstract
In this study, an aptamer-based single particle method was developed for the thrombin detection in human serum samples using fluorescence correlation spectroscopy (FCS). In this method, quantum dots (QDs) were used as the fluorescent probes and thrombin-binding aptamer (TBA) was used as molecular recognition unit. When two QDs probes labeled with TBA (QD-TBA1 and QD-TBA2) are mixed in a sample containing thrombin targets, the binding of targets will cause QDs to form dimers (or oligomers) with bigger sizes, which leads to the nearly double increase in the characteristic diffusion time of QDs in the detection volume of FCS. FCS method can detect the change in the characteristic diffusion time of QDs. Firstly, the diffusion and blinking behaviors of QD-TBA probes in the presence of thrombin were investigated by FCS and total internal reflection fluorescence microscopy (TIRFM) imaging system, and the experimental results documented that QD-TBAs were bound together with "one-by-one" structure when thrombin were added into the solution. And then, the assay conditions were optimized in order to improve the sensitivity and specificity of this method. Under the optimized conditions, the linear range of the method is from 5.0 nM to 500 nM of thrombin, and the limit of detection is about 2.6 nM. Finally, this method was applied to homogeneous determination of thrombin in human serum samples.
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Affiliation(s)
- Jinjin Yin
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Aidi Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
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137
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Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
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138
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Wang X, Jiang A, Hou T, Li H, Li F. Enzyme-free and label-free fluorescence aptasensing strategy for highly sensitive detection of protein based on target-triggered hybridization chain reaction amplification. Biosens Bioelectron 2015; 70:324-9. [PMID: 25840018 DOI: 10.1016/j.bios.2015.03.053] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/24/2022]
Abstract
Proteins are of great importance in medical and biological fields. In this paper, a novel fluorescent aptasensing strategy for protein assay has been developed based on target-triggered hybridization chain reaction (HCR) and graphene oxide (GO)-based selective fluorescence quenching. Three DNA probes, a helper DNA probe (HP), hairpin probe 1 (H1) and hairpin probe 2 (H2) are ingeniously designed. In the presence of the target, the aptamer sequences in HP recognize the target to form a target-aptamer complex, which causes the HP conformation change, and then triggers the chain-like assembly of H1 and H2 through the hybridization chain reaction, generating a long chain of HP leading complex of H1 and H2. At last the fluorescence indicator SYBR Green I (SG) binds with the long double strands of the HCR product through both intercalation and minor groove binding. When GO was added into the solutions after HCR, the free H1, H2 and SG would be closely adsorbed onto GO surface via π-π stacking. However, the HCR product cannot be adsorbed on GO surface, thereby the SG bound to HCR product gives a strong fluorescence signal dependent on the concentration of the target. With the use of platelet-derived growth factor BB (PDGF-BB) as the model analyte, this newly designed protocol provides a highly sensitive fluorescence detection of PDGF-BB with a limit of detection down to 1.25 pM, and also exhibit good selectivity and applicability in complex matrixes. Therefore, the proposed aptasensing strategy based on target-triggered hybridization chain reaction amplification should have wide applications in the diagnosis of genetic diseases due to its simplicity, low cost, and high sensitivity at extremely low target concentrations.
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Affiliation(s)
- Xiuzhong Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Aiwen Jiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ting Hou
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyin Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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139
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Sanzani SM, Reverberi M, Fanelli C, Ippolito A. Detection of ochratoxin A using molecular beacons and real-time PCR thermal cycler. Toxins (Basel) 2015; 7:812-20. [PMID: 25760080 PMCID: PMC4379526 DOI: 10.3390/toxins7030812] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 01/02/2023] Open
Abstract
We developed a simple and cheap assay for quantitatively detecting ochratoxin A (OTA) in wine. A DNA aptamer available in literature was used as recognition probe in its molecular beacon form, i.e., with a fluorescence-quenching pair at the stem ends. Our aptabeacon could adopt a conformation allowing OTA binding, causing a fluorescence rise due to the increased distance between fluorophore and quencher. We used real-time PCR equipment for capturing the signal. With this assay, under optimized conditions, the entire process can be completed within 1 h. In addition, the proposed system exhibited a good selectivity for OTA against other mycotoxins (ochratoxin B and aflatoxin M1) and limited interference from aflatoxin B1 and patulin. A wide linear detection range (0.2–2000 µM) was achieved, with LOD = 13 nM, r = 0.9952, and R2 = 0.9904. The aptabeacon was also applied to detect OTA in red wine spiked with the same dilution series. A linear correlation with a LOD = 19 nM, r = 0.9843, and R2 = 0.9708 was observed, with recoveries in the range 63%–105%. Intra- and inter-day assays confirmed its reproducibility. The proposed biosensor, although still being finalized, might significantly facilitate the quantitative detection of OTA in wine samples, thus improving their quality control from a food safety perspective.
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Affiliation(s)
- Simona Marianna Sanzani
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy.
| | - Massimo Reverberi
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
| | - Corrado Fanelli
- Department of Environmental Biology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
| | - Antonio Ippolito
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy.
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140
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Jebali A, Hekmatimoghaddam S, Kazemi B, De La Fuente JM. Presentation of a nano-based tag for immunoassay, based on amine-modified bovine serum albumin nanoparticles. IET Nanobiotechnol 2015; 9:43-51. [PMID: 25650325 DOI: 10.1049/iet-nbt.2014.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate four immunoassays, based on amine-modified bovine serum albumin nanoparticles (AMBSANPs). First, the capability of nitrate absorption by AMBSANPs under different conditions was evaluated. Then, serial concentrations of pure βHCG were added to wells coated with βHCG antibody for immunoassays 1 and 2, and wells coated with βHCG aptamer for immunoassays 3 and 4. Next, AMBSANPs conjugated with βHCG antibody was added for immunoassays 1 and 3, and AMBSANPs conjugated with βHCG aptamer were added for immunoassays 2 and 4. Finally, the optical density (OD) of each well was read at 340 nm, and compared with controls. Moreover, the concentration of βHCG in the clinical samples was quantified by immunoassays 1, 2, 3, 4 and ELISA, and then compared. The effect of some serum interferences on these immunoassay methods was evaluated. The authors observed that the amount of nitrate absorption by AMBSANPs increased with an increase in H+ ion concentration and temperature, and decreased with an increase in ion strength. The correlation (R2) between ELISA and immunoassays 1, 2, 3 and 4 were 0.97, 0.97, 0.98, 0.99, respectively. It was found that the increase in the serum interferences led to a decrease in the measured βHCG concentration.
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Affiliation(s)
- Ali Jebali
- Department of Medical Nanotechnology, Pajoohesh Lab, Yazd, Iran
| | - Seyedhossein Hekmatimoghaddam
- Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Bahram Kazemi
- Department of Biotechnology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Jesus Martinez De La Fuente
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of the Ministry of Education, Research Institute of Translation Medicine, Shanghai Jiao Tong University, Dongchuan Road 800, 200240 Shanghai, People's Republic of China
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141
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Wickramaratne TM, Pierre VC. Turning an aptamer into a light-switch probe with a single bioconjugation. Bioconjug Chem 2014; 26:63-70. [PMID: 25427946 PMCID: PMC4306522 DOI: 10.1021/bc5003899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
describe a method for transforming a structure-switching aptamer
into a luminescent light-switch probe via a single conjugation. The
methodology is demonstrated using a known aptamer for Hg2+ as a case study. This approach utilizes a lanthanide-based metallointercalator,
Eu-DOTA-Phen, whose luminescence is quenched almost entirely and selectively
by purines, but not at all by pyrimidines. This complex, therefore,
does not luminesce while intercalated in dsDNA, but it is bright red
when conjugated to a ssDNA that is terminated by several pyrimidines.
In its design, the light-switch probe incorporates a structure-switching
aptamer partially hybridized to its complementary strand. The lanthanide
complex is conjugated to either strand via a stable amide bond. Binding
of the analyte by the structure-switching aptamer releases the complementary
strand. This release precludes intercalation of the intercalator in
dsDNA, which switches on its luminescence. The resulting probe turns
on 21-fold upon binding to its analyte. Moreover, the structure switching
aptamer is highly selective, and the long luminescence lifetime of
the probe readily enables time-gating experiments for removal of the
background autofluorescence of the sample.
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142
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Saberian-Borujeni M, Johari-Ahar M, Hamzeiy H, Barar J, Omidi Y. Nanoscaled aptasensors for multi-analyte sensing. ACTA ACUST UNITED AC 2014; 4:205-15. [PMID: 25671177 PMCID: PMC4298712 DOI: 10.15171/bi.2014.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/03/2014] [Accepted: 11/08/2014] [Indexed: 12/21/2022]
Abstract
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Introduction: Nanoscaled aptamers (Aps), as short single-stranded DNA or RNA oligonucleotides, are able to bind to their specific targets with high affinity, upon which they are considered as powerful diagnostic and analytical sensing tools (the so-called "aptasensors"). Aptamers are selected from a random pool of oligonucleotides through a procedure known as "systematic evolution of ligands by exponential enrichment".
Methods: In this work, the most recent studies in the field of aptasensors are reviewed and discussed with a main focus on the potential of aptasensors for the multianalyte detection(s).
Results: Due to the specific folding capability of aptamers in the presence of analyte, aptasensors have substantially successfully been exploited for the detection of a wide range of small and large molecules (e.g., drugs and their metabolites, toxins, and associated biomarkers in various diseases) at very low concentrations in the biological fluids/samples even in presence of interfering species.
Conclusion: Biological samples are generally considered as complexes in the real biological media. Hence, the development of aptasensors with capability to determine various targets simultaneously within a biological matrix seems to be our main challenge. To this end, integration of various key scientific dominions such as bioengineering and systems biology with biomedical researches are inevitable.
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Affiliation(s)
- Mehdi Saberian-Borujeni
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Johari-Ahar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Hamzeiy
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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143
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Choi JS, Bae S, Kim KH, Seo TS. A large-area hemispherical perforated bead microarray for monitoring bead based aptamer and target protein interaction. BIOMICROFLUIDICS 2014; 8:064119. [PMID: 25587373 PMCID: PMC4290684 DOI: 10.1063/1.4903939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
Herein, we present a large-area 3D hemispherical perforated microwell structure for a bead based bioassay. Such a unique microstructure enables us to perform the rapid and stable localization of the beads at the single bead level and the facile manipulation of the bead capture and retrieval with high speed and efficiency. The fabrication process mainly consisted of three steps: the convex micropatterned nickel (Ni) mold production from the concave micropatterned silicon (Si) wafer, hot embossing on the polymer matrix to generate the concave micropattened acrylate sheet, and reactive ion etching to make the bottom holes. The large-area hemispherical perforated micropatterned acrylate sheet was sandwiched between two polydimethylsiloxane (PDMS) microchannel layers. The bead solution was injected and recovered in the top PDMS microchannel, while the bottom PDMS microchannel was connected with control lines to exert the hydrodynamic force in order to alter the flow direction of the bead solution for the bead capture and release operation. The streptavidin-coated microbead capture was achieved with almost 100% yield within 1 min, and all the beads were retrieved in 10 s. Lysozyme or thrombin binding aptamer labelled microbeads were trapped on the proposed bead microarray, and the in situ fluorescence signal of the bead array was monitored after aptamer-target protein interaction. The protein-aptamer conjugated microbeads were recovered, and the aptamer was isolated for matrix assisted laser desorption/ionization time-of-flight mass spectrometry analysis to confirm the identity of the aptamer.
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Affiliation(s)
- Jong Seob Choi
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
| | - Sunwoong Bae
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
| | - Kyung Hoon Kim
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) , 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
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144
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Wang X, Jiang A, Hou T, Li F. A sensitive and versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch. Analyst 2014; 139:6272-8. [PMID: 25319505 DOI: 10.1039/c4an01320d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, a versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch has been developed. An aptamer probe is designed to hybridize with the methylene blue (MB)-modified DNA capture probe immobilized on the gold electrode to form rigid triple-helix DNA, impeding the efficient electron transfer of MB to the electrode and resulting in the decreased oxidation peak current of MB. However, upon introduction of the perfectly matched target, for example, human α-thrombin (Tmb), the interaction between Tmb and the aptamer probe leads to the dissociation of the triple-helix DNA structure and thereby liberates the MB-modified end of the capture probe, allowing the MB to collide with the electrode surface and resulting in an increase of the oxidation peak currents of MB. Therefore, the sensitive signal-on detection of Tmb is realized, and the detection limit of Tmb is 0.12 nM. The proposed approach also demonstrates excellent regenerability, reproducibility and stability. Additionally, it also has the advantages of simplicity in design and easy operation. The success in the present biosensor provides a promising alternative to the electrochemical detection of a variety of analytes and may have potential applications in point-of-care testing and clinical diagnosis.
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Affiliation(s)
- Xiuzhong Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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145
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Armstrong RE, Strouse GF. Rationally manipulating aptamer binding affinities in a stem-loop molecular beacon. Bioconjug Chem 2014; 25:1769-76. [PMID: 25170558 PMCID: PMC4198099 DOI: 10.1021/bc500286r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Single-stranded
DNA sequences that are highly specific for a target
ligand are called aptamers. While the incorporation of aptamer sequences
into stem-loop molecular beacons has become an essential tool in optical
biosensors, the design principles that determine the magnitude of
binding affinity and its relationship to placement of the aptamer
sequence in the stem-loop architecture are not well defined. By controlled
placement of the aptamer along the loop region of the molecular beacon,
it is observed that the binding affinity can be tuned over 4 orders
of magnitude (1.3 nM – 203 μM) for the Huizenga and Szostak
ATP DNA aptamer sequence. It is observed that the Kd is enhanced for the fully exposed sequence, with reduced
binding affinity when the aptamer is part of the stem region of the
beacon. Analysis of the ΔG values indicate
a clear correlation between the aptamer hybridized length in the stem
and its observed Kd. The use of a nanometal
surface energy transfer probe method for monitoring ATP binding to
the aptamer sequence allows the observation of negative cooperativity
between the two ATP binding events. Maintenance of the high binding
affinity of this ATP aptamer and the observation of two separate Kd’s for ATP binding indicate NSET as
an effective, nonmanipulative, optical method for tracking biomolecular
changes.
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Affiliation(s)
- Rachel E Armstrong
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftan Way, Room 118 DLC, Tallahassee, Florida 32306, United States
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146
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Catherine AT, Shishido SN, Robbins-Welty GA, Diegelman-Parente A. Rational design of a structure-switching DNA aptamer for potassium ions. FEBS Open Bio 2014; 4:788-95. [PMID: 25352996 PMCID: PMC4209343 DOI: 10.1016/j.fob.2014.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/20/2014] [Accepted: 08/30/2014] [Indexed: 11/18/2022] Open
Abstract
We report the rational design of structure-switching DNA aptamers for potassium. The shift between non-binding and binding-competent states was determined experimentally. The stability of the non-binding state was estimated computationally. A linear free energy relationship between these values was established.
Structure-switching molecules provide a unique means for analyte detection, generating a response to analyte concentration through a binding-specific conformational change between non-binding and binding-competent states. While most ligand-binding molecules are not structure switching by default, many can be engineered to be so through the introduction of an alternative non-binding (and thus non-signalling) conformation. This population-shift mechanism is particularly effective with oligonucleotides and has led to the creation of structure-switching aptamers for many target ligands. Here, we report the rational design of structure-switching DNA aptamers, based on the thrombin binding aptamer (TBA), that bind potassium with affinities that bridge the gap between previously reported weak-binding and strong-binding aptamers. We also demonstrate a correlation between the free energy of the experimentally determined binding affinity for potassium and the computationally estimated free energy of the alternative (non-binding) structure.
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Affiliation(s)
- Andrew T. Catherine
- Department of Chemistry, Penn State Altoona, Altoona, PA 16601, United States
| | | | - Gregg A. Robbins-Welty
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA 16546, United States
| | - Amy Diegelman-Parente
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA 16546, United States
- Corresponding author. Tel./fax: +1 814 824 3876.
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147
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Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 2014; 15:1-10. [DOI: 10.1111/1567-1364.12188] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Redden
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
| | - Nicholas Morse
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
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148
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Zhang K, Tan T, Fu JJ, Zheng T, Zhu JJ. A novel aptamer-based competition strategy for ultrasensitive electrochemical detection of leukemia cells. Analyst 2014; 138:6323-30. [PMID: 23978949 DOI: 10.1039/c3an01255g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A robust, nanobiotechnology-based electrochemical cytosensing platform for the detection of acute leukemia cells was developed with high sensitivity, selectivity, acceptable rapidity and excellent extensibility. It utilized the competitive binding of cell-specific aptamers to acute leukemia cells and subsequent voltammetric quantification of the metal signature. Greatly enhanced sensitivity was achieved with dual signal amplification by using Fe3O4 magnetic nanoparticles (MNPs) as carriers to load a large amount of gold nanoparticles (AuNPs) and AuNP-catalyzed silver deposition. The proposed competitive cytosensor showed high sensitivity with a detection limit down to 10 cells. This simple and low-cost electrochemical cytosensing approach offers great promise to extend its application to early detection of human leukemia and possibly to other cancer cells.
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Affiliation(s)
- Kui Zhang
- The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, 210008, P. R. China
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149
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Oishi M, Nakao S, Kato D. Enzyme-free fluorescent-amplified aptasensors based on target-responsive DNA strand displacement via toehold-mediated click chemical ligation. Chem Commun (Camb) 2014; 50:991-3. [PMID: 24306006 DOI: 10.1039/c3cc48064j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new target-responsive DNA strand displacement system via toehold-mediated click chemical ligation was designed and prepared for enzyme-free fluorescent-amplified aptasensors. The aptasensors significantly amplified fluorescent signals in response to targets based on target recycling processes.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan.
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150
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Trevino SG, Levy M. High-throughput bead-based identification of structure-switching aptamer beacons. Chembiochem 2014; 15:1877-81. [PMID: 25056925 PMCID: PMC4161366 DOI: 10.1002/cbic.201402037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 12/29/2022]
Abstract
We describe a new platform to identify structure-switching DNA beacon aptamers, which detect small molecules in a specific manner. By clonally amplifying a DNA library designed to fluoresce in response to binding events onto microbeads, aptamer beacons can be selected by stringent fluorescence-assisted sorting. We validated this method by isolating known and novel anti-steroid aptamers from two separate DNA libraries that were structurally enriched with three-way junctions. Importantly, aptamers were retrieved in only a few (three) rounds of selection by this approach and did not require further optimization, significantly streamlining the process of beacon development.
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Affiliation(s)
- Simon G Trevino
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 (USA)
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