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Aptamers as Synthetic Receptors for Food Quality and Safety Control. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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152
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Heemstra JM. Learning from the unexpected in life and DNA self-assembly. Beilstein J Org Chem 2015; 11:2713-20. [PMID: 26877793 PMCID: PMC4734352 DOI: 10.3762/bjoc.11.292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/07/2015] [Indexed: 01/09/2023] Open
Abstract
The greatest lessons in life and science often arise from the unexpected. Thus, rather than viewing these experiences as hindering our progress, they should be embraced and appreciated for their ability to lead to new discoveries. In this perspective, I will discuss the unexpected events that have shaped my career path and the early stages of my independent research program.
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Affiliation(s)
- Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
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153
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Shrivastava S, Sohn IY, Son YM, Lee WI, Lee NE. Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform. NANOSCALE 2015; 7:19663-19672. [PMID: 26553481 DOI: 10.1039/c5nr05839b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.
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Affiliation(s)
- Sajal Shrivastava
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea.
| | - Il-Yung Sohn
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea.
| | - Young-Min Son
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea.
| | - Won-Il Lee
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea.
| | - Nae-Eung Lee
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea. and SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea
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154
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Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection. Molecules 2015; 20:21298-312. [PMID: 26633328 PMCID: PMC6332362 DOI: 10.3390/molecules201219766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/21/2015] [Accepted: 11/12/2015] [Indexed: 01/05/2023] Open
Abstract
The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR) and Fluorescence Activated Cell Sorting (FACS) to high-throughput selection techniques. Within these systems, monoclonal aptamer microbeads can be individually generated and assayed to assess aptamer candidate fitness thereby helping eliminate stochastic effects which are common to classical SELEX techniques. Such techniques have given rise to aptamers with 1000 times greater binding affinities when compared to traditional SELEX. Another emerging technique is Fluorescence Activated Droplet Sorting (FADS) whereby selection does not rely on binding capture allowing evolution of a greater diversity of aptamer properties such as fluorescence or enzymatic activity. Within this review we explore examples and applications of oligonucleotide functionalised microbeads in aptamer selection and reflect upon new opportunities arising for aptamer science.
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155
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Wang P, Wan Y, Ali A, Deng S, Su Y, Fan C, Yang S. Aptamer-wrapped gold nanoparticles for the colorimetric detection of omethoate. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5488-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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156
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Cansiz S, Zhang L, Wu C, Wu Y, Teng IT, Hou W, Wang Y, Wan S, Cai R, Jin C, Liu Q, Tan W. DNA Aptamer Based Nanodrugs: Molecular Engineering for Efficiency. Chem Asian J 2015; 10:2084-94. [PMID: 26177853 DOI: 10.1002/asia.201500434] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 12/21/2022]
Abstract
In the past two decades, the study of cancer therapy has gradually advanced to the "nano" era. Numerous novel nanomaterials armed with unique physical properties have been introduced into biomedical research. At the same time, functional nucleic acid molecules, especially aptamers, have aroused broad attention from the biomedical community. Benefiting from the advancement of molecular engineering strategies, it is now feasible to combine the cancer-specific recognition capability of aptamers with various other special functions of nanomaterials to develop cancer-specific drugs at the nanoscale. Nanodrugs are now offering an unprecedented opportunity to achieve the goal of efficient targeted delivery as well as controlled release. This review highlights some achievements made in multiple aptamer-based nanodrug systems that have emerged in recent years, including studies in the infant stage of "proof-of-concept".
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Affiliation(s)
- Sena Cansiz
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Liqin Zhang
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Cuichen Wu
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Yuan Wu
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - I-Ting Teng
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Weijia Hou
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Yanyue Wang
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Shuo Wan
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Ren Cai
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Chen Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Weihong Tan
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA. .,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China.
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157
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Fiore E, Dausse E, Dubouchaud H, Peyrin E, Ravelet C. Ultrafast capillary electrophoresis isolation of DNA aptamer for the PCR amplification-based small analyte sensing. Front Chem 2015; 3:49. [PMID: 26322305 PMCID: PMC4533002 DOI: 10.3389/fchem.2015.00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/27/2015] [Indexed: 01/14/2023] Open
Abstract
Here, we report a new homogeneous DNA amplification-based aptamer assay for small analyte sensing. The aptamer of adenosine chosen as the model analyte was split into two fragments able to assemble in the presence of target. Primers were introduced at extremities of one fragment in order to generate the amplifiable DNA component. The amount of amplifiable fragment was quantifiable by Real-Time Polymerase Chain Reaction (RT-PCR) amplification and directly reliable on adenosine concentration. This approach combines the very high separation efficiency and the homogeneous format (without immobilization) of capillary electrophoresis (CE) and the sensitivity of real time PCR amplification. An ultrafast isolation of target-bound split aptamer (60 s) was developed by designing a CE input/ouput scheme. Such method was successfully applied to the determination of adenosine with a LOD of 1 μM.
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Affiliation(s)
- Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Eric Dausse
- Laboratoire ARNA, Institut National de la Santé et de la Recherche Médicale U869, Université Bordeaux Bordeaux, France
| | - Hervé Dubouchaud
- Laboratoire de Bioénergétique Fondamentale et Appliquée, Institut National de la Santé et de la Recherche Médicale U1055, University Grenoble Alpes Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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158
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Zhao T, Liu R, Ding X, Zhao J, Yu H, Wang L, Xu Q, Wang X, Lou X, He M, Xiao Y. Nanoprobe-Enhanced, Split Aptamer-Based Electrochemical Sandwich Assay for Ultrasensitive Detection of Small Molecules. Anal Chem 2015; 87:7712-9. [PMID: 26171721 DOI: 10.1021/acs.analchem.5b01178] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is quite challenging to improve the binding affinity of antismall molecule aptamers. We report that the binding affinity of anticocaine split aptamer pairs improved by up to 66-fold by gold nanoparticles (AuNP)-attached aptamers due to the substantially increased local concentration of aptamers and multiple and simultaneous ligand interactions. The significantly improved binding affinity enables the detection of small molecule targets with unprecedented sensitivity, as demonstrated in nanoprobe-enhanced split aptamer-based electrochemical sandwich assays (NE-SAESA). NE-SAESA replaces the traditional molecular reporter probe with AuNPs conjugated to multiple reporter probes. The increased binding affinity allowed us to use 1,000-fold lower reporter probe concentrations relative to those employed in SAESA. We show that the near-elimination of background in NE-SAESA effectively improves assay sensitivity by ∼1,000-100,000-fold for ATP and cocaine detection, relative to equivalent SAESA. With the ongoing development of new strategies for the selection of aptamers, we anticipate that our sensor platform should offer a generalizable approach for the high-sensitivity detection of diverse targets. More importantly, we believe that NE-SAESA represents a novel strategy to improve the binding affinity between a small molecule and its aptamer and potentially can be extended to other detection platforms.
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Affiliation(s)
- Tao Zhao
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Ran Liu
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xiaofan Ding
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Juncai Zhao
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Haixiang Yu
- ‡Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Lei Wang
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Qing Xu
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xuan Wang
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xinhui Lou
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Miao He
- §School of Environment, Tsinghua University, Beijing 100084, China
| | - Yi Xiao
- ‡Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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159
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Zhou W, Huang PJJ, Ding J, Liu J. Aptamer-based biosensors for biomedical diagnostics. Analyst 2015; 139:2627-40. [PMID: 24733714 DOI: 10.1039/c4an00132j] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.
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Affiliation(s)
- Wenhu Zhou
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Central South University, Tongzipo Road #172, Changsha 410013, Hunan, PR China.
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160
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An improved design of the kissing complex-based aptasensor for the detection of adenosine. Anal Bioanal Chem 2015; 407:6515-24. [DOI: 10.1007/s00216-015-8818-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/16/2015] [Accepted: 06/01/2015] [Indexed: 01/01/2023]
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161
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Barros SA, Chenoweth DM. Triptycene-based small molecules modulate (CAG)·(CTG) repeat junctions. Chem Sci 2015; 6:4752-4755. [PMID: 26366282 PMCID: PMC4538686 DOI: 10.1039/c5sc01595b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 05/27/2015] [Indexed: 01/19/2023] Open
Abstract
A triptycene-based scaffold is used to develop a new class of ligands for modulating the structure of junction forming trinucleotide repeat expansion sequences.
Nucleic acid three-way junctions (3WJs) play key roles in biological processes such as nucleic acid replication in addition to being implicated as dynamic transient intermediates in trinucleotide repeat sequences. Structural modulation of specific nucleic acid junctions could allow for control of biological processes and disease states at the nucleic acid level. Trinucleotide repeat expansions are associated with several neurodegenerative diseases where dynamic slippage is thought to occur during replication, forming transient 3WJ intermediates with the complementary strand. Here, we report triptycene-based molecules that bind to a d(CAG)·(CTG) repeat using a gel shift assay, fluorescence-quenching and circular dichroism.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104-6323 , USA .
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104-6323 , USA .
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162
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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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163
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Neves MAD, Blaszykowski C, Bokhari S, Thompson M. Ultra-high frequency piezoelectric aptasensor for the label-free detection of cocaine. Biosens Bioelectron 2015; 72:383-92. [PMID: 26022784 DOI: 10.1016/j.bios.2015.05.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/30/2015] [Accepted: 05/16/2015] [Indexed: 11/26/2022]
Abstract
This paper describes a label-free and real-time piezoelectric aptasensor for the detection of cocaine. The acoustic wave sensing platform is a quartz substrate functionalized with an adlayer of S-(11-trichlorosilyl-undecanyl)-benzenethiosulfonate (BTS) cross-linker onto which the anti-cocaine MN4 DNA aptamer is next immobilized. Preparation of the sensor surface was monitored using X-ray photoelectron spectroscopy (XPS), while the binding of cocaine to surface-attached MN4 was evaluated using the electromagnetic piezoelectric acoustic sensor (EMPAS). The MN4 aptamer, unlike other cocaine aptamer variants, has its secondary structure preformed in the unbound state with only tertiary structure changes occurring during target binding. It is postulated that the highly sensitive EMPAS detected the binding of cocaine through target mass loading coupled to aptamer tertiary structure folding. The sensor achieved an apparent Kd of 45 ± 12 µM, and a limit of detection of 0.9 µM. Repeated regenerability of the sensor platform was also demonstrated. This work constitutes the first application of EMPAS technology in the field of aptasensors. Furthermore, it is so far one of the very few examples of a bulk acoustic wave aptasensor that is able to directly detect the binding interaction between an aptamer and a small molecule in a facile one-step protocol without the use of a complex assay or signal amplification step.
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Affiliation(s)
- Miguel A D Neves
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
| | | | - Sumra Bokhari
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Michael Thompson
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6; Econous Systems Inc., 80 St. George Street, Toronto, Ontario, Canada M5S 3H6; Institute for Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9.
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164
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Slavkovic S, Altunisik M, Reinstein O, Johnson PE. Structure-affinity relationship of the cocaine-binding aptamer with quinine derivatives. Bioorg Med Chem 2015; 23:2593-7. [PMID: 25858454 DOI: 10.1016/j.bmc.2015.02.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022]
Abstract
In addition to binding its target molecule, cocaine, the cocaine-binding aptamer tightly binds the alkaloid quinine. In order to understand better how the cocaine-binding aptamer interacts with quinine we have used isothermal titration calorimetry-based binding experiments to study the interaction of the cocaine-binding aptamer to a series of structural analogs of quinine. As a basis for comparison we also investigated the binding of the cocaine-binding aptamer to a set of cocaine metabolites. The bicyclic aromatic ring on quinine is essential for tight affinity by the cocaine-binding aptamer with 6-methoxyquinoline alone being sufficient for tight binding while the aliphatic portion of quinine, quinuclidine, does not show detectable binding. Compounds with three fused aromatic rings are not bound by the aptamer. Having a methoxy group at the 6-position of the bicyclic ring is important for binding as substituting it with a hydrogen, an alcohol or an amino group all result in lower binding affinity. For all ligands that bind, association is driven by a negative enthalpy compensated by unfavorable binding entropy.
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Affiliation(s)
- Sladjana Slavkovic
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Merve Altunisik
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Oren Reinstein
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada.
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165
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Yang C, Spinelli N, Perrier S, Defrancq E, Peyrin E. Macrocyclic host-dye reporter for sensitive sandwich-type fluorescent aptamer sensor. Anal Chem 2015; 87:3139-43. [PMID: 25738735 DOI: 10.1021/acs.analchem.5b00341] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe herein a novel approach for the fluorescent detection of small molecules using a sandwich-type aptamer strategy based on a signaling macrocyclic host-dye system. One split adenosine aptamer fragment was 5'-conjugated to a β-cylodextrin (CD) molecule while the other nucleic acid fragment was labeled at the 3'-end by a dansyl molecule prone to be included into the macrocycle. The presence of the small target analyte governed the assembly of the two fragments, bringing the dye molecule and its specific receptor in close proximity and promoting the inclusion interaction. Upon the inclusion complex formation, the microenvironment of dansyl was modified in such a way that the fluorescent intensity increased. Concomitantly, this supplementary interaction at the aptamer extremities induced stabilizing effects on the ternary complex. We next proposed a bivalent signaling design where the two extremities of one split aptamer fragment were conjugated to the β-CD molecule while those of the other fragment were tagged by the dansyl dye. The dual reporting dye inclusion promoted an improvement of both the signal-to-background change and the assay sensitivity. Owing to the vast diversity of responsive host-macrocycle systems available, this aptasensor strategy has potential to be extended to the multiplexed analysis and to other kinds of transducers (such as electrochemical).
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Affiliation(s)
- Cheng Yang
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France.,‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Nicolas Spinelli
- ‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Sandrine Perrier
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Eric Defrancq
- ‡Université Grenoble Alpes, CNRS, DCM UMR 5250, F-38041 Grenoble, France
| | - Eric Peyrin
- †Université Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France
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166
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Dereli Ö, Bahçeli S, Abbas A, Naseer MM. Quantum chemical investigations of a co-crystal of 1,3,5-tris(4-hydroxyphenyl)benzene and 2,4,6-trimethoxy-1,3,5-triazine. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1413-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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167
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Cheng F, He Y, Xing XJ, Tan DD, Lin Y, Pang DW, Tang HW. A gold nanoparticle-based label free colorimetric aptasensor for adenosine deaminase detection and inhibition assay. Analyst 2015; 140:1572-7. [PMID: 25597304 DOI: 10.1039/c4an02070g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strategy for the fabrication of a colorimetric aptasensor using label free gold nanoparticles (AuNPs) is proposed in this work, and the strategy has been employed for the assay of adenosine deaminase (ADA) activity. The aptasensor consists of adenosine (AD) aptamer, AD and AuNPs. The design of the biosensor takes advantage of the special optical properties of AuNPs and the interaction between AuNPs and single-strand DNA. In the absence of ADA, the AuNPs are aggregated and are blue in color under appropriate salt concentration because of the grid structure of an AD aptamer when binding to AD, while in the presence of the analyte, AuNPs remain dispersed with red color under the same concentration of salt owing to ADA converting AD into inosine which has no affinity with the AD aptamer, thus allowing quantitative investigation of ADA activity. The present strategy is simple, cost-effective, selective and sensitive for ADA with a detection limit of 1.526 U L(-1), which is about one order of magnitude lower than that previously reported. In addition, a very low concentration of the inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) could generate a distinguishable response. Therefore, the AuNP-based colorimetric biosensor has great potential in the diagnosis of ADA-relevant diseases and drug screening.
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Affiliation(s)
- Fen Cheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, and Wuhan Institute of Biotechnology, Wuhan University, Wuhan, 430072, P. R. China.
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168
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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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169
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Zhang S, Hu X, Yang X, Sun Q, Xu X, Liu X, Shen G, Lu J, Shen G, Yu R. Background eliminated signal-on electrochemical aptasensing platform for highly sensitive detection of protein. Biosens Bioelectron 2014; 66:363-9. [PMID: 25463644 DOI: 10.1016/j.bios.2014.11.044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 12/29/2022]
Abstract
Using platelet-derived growth factor B chain dimer (PDGF-BB) as the model target, a background current eliminated electrochemical aptameric sensing platform for highly sensitive and signal-on detection of protein is proposed in this paper. Successful fabrication of the biosensor depends on ingenious design of aptamer probe, which contains the aptamer sequence for PDGF-BB and the recognition sequence for EcoRI endonuclease. In the absence of PDGF-BB, the ferrocene labeled aptamer probe folds into a hairpin structure and forms a recognition site for EcoRI. By treatment with endonuclease, the specific and cleavable double-stranded region is cut off and redox-active ferrocene molecule is removed from the electrode surface, and almost no peak current is observed. When binding with target protein, the designed aptamer probe changes its conformation and dissociates the recognition double strand. The integrated aptamer probe is maintained when exposing to EcoRI endonuclease, resulting in obvious peak current. Therefore, a signal-on and sensitive sensing strategy for PDGF-BB detection is fabricated with eliminated background current. Under the optimized experimental conditions, a wide linear response range of 4 orders of magnitude from 20pgmL(-1) to 200ngmL(-1) is achieved with a detection limit of 10pgmL(-1). Moreover, the present aptameric platform is universal for the analysis of a broad range of target molecules of interest by changing and designing the sequence of aptamer probe.
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Affiliation(s)
- Songbai Zhang
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
| | - Xia Hu
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Xiaohui Yang
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Qinli Sun
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Xiaolin Xu
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Xuewen Liu
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Guangyu Shen
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Jilin Lu
- Department of Chemistry and Chemical Engineering, Hunan University of Arts and Science, Changde 415000, PR China
| | - Guoli Shen
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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170
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Xu X, Yang X. Reversion of DNA strand displacement using functional nucleic acids as toeholds. Chem Commun (Camb) 2014; 50:805-7. [PMID: 24292558 DOI: 10.1039/c3cc47102k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein we report the reversion of DNA strand displacement using functional nucleic acids as toeholds.
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Affiliation(s)
- Xiaowen Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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171
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Roncancio D, Yu H, Xu X, Wu S, Liu R, Debord J, Lou X, Xiao Y. A label-free aptamer-fluorophore assembly for rapid and specific detection of cocaine in biofluids. Anal Chem 2014; 86:11100-6. [PMID: 25342426 DOI: 10.1021/ac503360n] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report a rapid and specific aptamer-based method for one-step cocaine detection with minimal reagent requirements. The feasibility of aptamer-based detection has been demonstrated with sensors that operate via target-induced conformational change mechanisms, but these have generally exhibited limited target sensitivity. We have discovered that the cocaine-binding aptamer MNS-4.1 can also bind the fluorescent molecule 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) and thereby quench its fluorescence. We subsequently introduced sequence changes into MNS-4.1 to engineer a new cocaine-binding aptamer (38-GC) that exhibits higher affinity to both ligands, with reduced background signal and increased signal gain. Using this aptamer, we have developed a new sensor platform that relies on the cocaine-mediated displacement of ATMND from 38-GC as a result of competitive binding. We demonstrate that our sensor can detect cocaine within seconds at concentrations as low as 200 nM, which is 50-fold lower than existing assays based on target-induced conformational change. More importantly, our assay achieves successful cocaine detection in body fluids, with a limit of detection of 10.4, 18.4, and 36 μM in undiluted saliva, urine, and serum samples, respectively.
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Affiliation(s)
- Daniel Roncancio
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
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172
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Barros SA, Chenoweth DM. Recognition of nucleic acid junctions using triptycene-based molecules. Angew Chem Int Ed Engl 2014; 53:13746-50. [PMID: 25257803 DOI: 10.1002/anie.201407061] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Indexed: 12/24/2022]
Abstract
The modulation of nucleic acids by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure-specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way junctions, providing a new scaffold for the development of nucleic acid junction binders with enhanced recognition properties. Additionally, we report cytotoxicity and cell uptake data in two human ovarian carcinoma cell lines.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 (USA)
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173
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Barros SA, Chenoweth DM. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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174
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Ahmad M, Pervez H, Ben Hadda T, Toupet L, Naseer MM. Synthesis and solid state self-assembly of an isatin–thiazoline hybrid driven by three self-complementary dimeric motifs. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.08.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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175
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Dokukin V, Silverman SK. A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains. Chem Commun (Camb) 2014; 50:9317-20. [PMID: 25000337 PMCID: PMC4126072 DOI: 10.1039/c4cc04253k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We assess the utility of integrating a predetermined aptamer DNA module adjacent to a random catalytic DNA region for identifying new deoxyribozymes by in vitro selection. By placing a known ATP aptamer next to an N40 random region, an explicitly modular DNA catalyst for tyrosine side chain phosphorylation is identified. The results have implications for broader identification of deoxyribozymes that function with small-molecule substrates.
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Affiliation(s)
- Victor Dokukin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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176
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Shen B, Li J, Cheng W, Yan Y, Tang R, Li Y, Ju H, Ding S. Electrochemical aptasensor for highly sensitive determination of cocaine using a supramolecular aptamer and rolling circle amplification. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1333-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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177
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Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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178
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Shen J, Li Y, Gu H, Xia F, Zuo X. Recent development of sandwich assay based on the nanobiotechnologies for proteins, nucleic acids, small molecules, and ions. Chem Rev 2014; 114:7631-77. [PMID: 25115973 DOI: 10.1021/cr300248x] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juwen Shen
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST) , Wuhan 430074, China
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179
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Yao J, Yang M, Duan Y. Chemistry, Biology, and Medicine of Fluorescent Nanomaterials and Related Systems: New Insights into Biosensing, Bioimaging, Genomics, Diagnostics, and Therapy. Chem Rev 2014; 114:6130-78. [DOI: 10.1021/cr200359p] [Citation(s) in RCA: 592] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jun Yao
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mei Yang
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yixiang Duan
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Research
Center of Analytical Instrumentation, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
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180
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Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 2014; 59:64-74. [PMID: 24690563 DOI: 10.1016/j.bios.2014.03.014] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 01/16/2023]
Abstract
Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.
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Affiliation(s)
- Chunjing Feng
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Shuang Dai
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China.
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181
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Zhao Q, Zhang Z, Xu L, Xia T, Li N, Liu J, Fang X. Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection. Anal Bioanal Chem 2014; 406:2949-55. [PMID: 24599422 DOI: 10.1007/s00216-014-7705-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/23/2014] [Accepted: 02/18/2014] [Indexed: 12/31/2022]
Abstract
A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.
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Affiliation(s)
- Qiuling Zhao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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182
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Yi X, Li L, Peng Y, Guo L. A universal electrochemical sensing system for small biomolecules using target-mediated sticky ends-based ligation-rolling circle amplification. Biosens Bioelectron 2014; 57:103-9. [PMID: 24561524 DOI: 10.1016/j.bios.2014.01.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/27/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
Abstract
A novel versatile electrochemical platform for ultrasensitive detection of small biomolecules was developed using ligation-rolling circle amplification (L-RCA) with analyte-mediated sticky ends. In order to achieve DNA cyclization, we designed two ss-DNA probes: the leftpart probe could form a "hairpin" structure by denaturing; the rightpart probe could also form a "hairpin" structure based on analyte-activated conformation change. Then the two probes with the same sticky ends (G-AATTC) could be ligated in the presence of Escherichia coli DNA ligase, forming a circular template for rolling circle amplification (RCA), which could be triggered by adding the primer probe and Phi29 DNA polymerase. Electrochemical impedance spectroscopy (EIS) was employed as the detection method. Overall, the proposed L-RCA-based sensing system not only exhibits excellent analytical characteristics with a detection limit of 320 pM and a linear range of 5 orders of magnitude (1 nM-10 μM), but also provides a universal design idea of L-RCA, which broadens the use of DNA amplification method and holds great promise in ultrasensitive bioassay in the future.
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Affiliation(s)
- Xiaohui Yi
- School of Chemistry & Environment, Beihang University, Xueyuan Road #37, Haidian District, Beijing 100191, China
| | - Lidong Li
- School of Chemistry & Environment, Beihang University, Xueyuan Road #37, Haidian District, Beijing 100191, China.
| | - Yi Peng
- School of Chemistry & Environment, Beihang University, Xueyuan Road #37, Haidian District, Beijing 100191, China
| | - Lin Guo
- School of Chemistry & Environment, Beihang University, Xueyuan Road #37, Haidian District, Beijing 100191, China.
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183
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Yoshida W, Abe K, Ikebukuro K. Emerging techniques employed in aptamer-based diagnostic tests. Expert Rev Mol Diagn 2014; 14:143-51. [PMID: 24400930 DOI: 10.1586/14737159.2014.868307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since aptamers were reported in 1990, research into the applications of aptamers, particularly diagnostic applications, has been growing. Aptamers can act as recognition elements instead of antibodies. In this regard, aptamers have unique characteristics because they are composed of nucleic acids. Intra- and intermolecular interactions of nucleic acids can be easily tailored following straightforward hybridization rules. Nucleic acids can be enzymatically replicated and their sequences can be determined using high-throughput methods. Using these properties, ligand-induced structural change-based aptamer sensors for homogeneous assays, polymerase- and/or nuclease-combined aptamer sensors for ultrasensitive assays, and microarray/next-generation sequencing-based aptamer sensors for multiplexed assays have been developed. This article reviews these unique aptamer sensors, demonstrating their great potential for diagnostic applications.
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Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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184
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Li S, Wang L, Hao Y, Zhang L, Zhou B, Deng L, Liu YN. An ultrasensitive colorimetric aptasensor for ATP based on peptide/Au nanocomposites and hemin–G-quadruplex DNAzyme. RSC Adv 2014. [DOI: 10.1039/c4ra02823f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A self-assembled peptide nanosphere was firstly applied to construct biosensors. A new signal amplification strategy was proposed for colorimetric aptasensor based on PNS/AuNPs composite. The colorimetric aptasensor displayed an ultra-high sensitivity for ATP detection with a LOD of 1.35 pM.
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Affiliation(s)
- Shipeng Li
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
| | - Liqiang Wang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
| | - Yuanqiang Hao
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
| | - Lili Zhang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
| | - Binbin Zhou
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
- Hunan Institute of Food Quality Supervision Inspection and Research
- Changsha, PR China
| | - Liu Deng
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
| | - You-Nian Liu
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha, PR China
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185
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Heo JH, Cho HH, Lee JH. Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing. Analyst 2014; 139:5936-44. [DOI: 10.1039/c4an01271b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.
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Affiliation(s)
- Jun Hyuk Heo
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Hui Hun Cho
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
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186
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Bing T, Mei H, Zhang N, Qi C, Liu X, Shangguan D. Exact tailoring of an ATP controlled streptavidin binding aptamer. RSC Adv 2014. [DOI: 10.1039/c4ra00714j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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187
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Reinstein O, Yoo M, Han C, Palmo T, Beckham SA, Wilce MCJ, Johnson PE. Quinine binding by the cocaine-binding aptamer. Thermodynamic and hydrodynamic analysis of high-affinity binding of an off-target ligand. Biochemistry 2013; 52:8652-62. [PMID: 24175947 DOI: 10.1021/bi4010039] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cocaine-binding aptamer is unusual in that it tightly binds molecules other than the ligand it was selected for. Here, we study the interaction of the cocaine-binding aptamer with one of these off-target ligands, quinine. Isothermal titration calorimetry was used to quantify the quinine-binding affinity and thermodynamics of a set of sequence variants of the cocaine-binding aptamer. We find that the affinity of the cocaine-binding aptamer for quinine is 30-40 times stronger than it is for cocaine. Competitive-binding studies demonstrate that both quinine and cocaine bind at the same site on the aptamer. The ligand-induced structural-switching binding mechanism of an aptamer variant that contains three base pairs in stem 1 is retained with quinine as a ligand. The short stem 1 aptamer is unfolded or loosely folded in the free form and becomes folded when bound to quinine. This folding is confirmed by NMR spectroscopy and by the short stem 1 construct having a more negative change in heat capacity of quinine binding than is seen when stem 1 has six base pairs. Small-angle X-ray scattering (SAXS) studies of the free aptamer and both the quinine- and the cocaine-bound forms show that, for the long stem 1 aptamers, the three forms display similar hydrodynamic properties, and the ab initio shape reconstruction structures are very similar. For the short stem 1 aptamer there is a greater variation among the SAXS-derived ab initio shape reconstruction structures, consistent with the changes expected with its structural-switching binding mechanism.
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Affiliation(s)
- Oren Reinstein
- Department of Chemistry, York University , 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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188
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Kent AD, Spiropulos NG, Heemstra JM. General approach for engineering small-molecule-binding DNA split aptamers. Anal Chem 2013; 85:9916-23. [PMID: 24033257 DOI: 10.1021/ac402500n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Here we report a general method for engineering three-way junction DNA aptamers into split aptamers. Split aptamers show significant potential for use as recognition elements in biosensing applications, but reliable methods for generating these sequences are currently lacking. We hypothesize that the three-way junction is a "privileged architecture" for the elaboration of aptamers into split aptamers, as it provides two potential splitting sites that are distal from the target binding pocket. We propose a general method for split aptamer engineering that involves removing one loop region, then systematically modifying the number of base pairs in the remaining stem regions in order to achieve selective assembly only in the presence of the target small molecule. We screen putative split aptamer sequence pairs using split aptamer proximity ligation (StAPL) technology developed by our laboratory, but we validate that the results obtained using StAPL translate directly to systems in which the aptamer fragments are assembling noncovalently. We introduce four new split aptamer sequences, which triples the number of small-molecule-binding DNA split aptamers reported to date, and the methods described herein provide a reliable route for the engineering of additional split aptamers, dramatically advancing the potential substrate scope of DNA assembly based biosensors.
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Affiliation(s)
- Alexandra D Kent
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112, United States
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189
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Jin F, Lian Y, Li J, Zheng J, Hu Y, Liu J, Huang J, Yang R. Molecule-binding dependent assembly of split aptamer and γ-cyclodextrin: a sensitive excimer signaling approach for aptamer biosensors. Anal Chim Acta 2013; 799:44-50. [PMID: 24091373 DOI: 10.1016/j.aca.2013.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/04/2013] [Accepted: 08/06/2013] [Indexed: 11/27/2022]
Abstract
A highly sensitive and selective fluorescence aptamer biosensors for the determination of adenosine triphosphate (ATP) was developed. Binding of a target with splitting aptamers labeled with pyrene molecules form stable pyrene dimer in the γ-cyclodextrin (γ-CD) cavity, yielding a strong excimer emission. We have found that inclusion of pyrene dimer in γ-cyclodextrin cavity not only exhibits additive increases in quantum yield and emission lifetime of the excimer, but also facilitates target-induced fusion of the splitting aptamers to form the aptamer/target complex. As proof-of-principle, the approach was applied to fluorescence detection of adenosine triphosphate. With an anti-ATP aptamer, the approach exhibits excimer fluorescence response toward ATP with a maximum signal-to-background ratio of 32.1 and remarkably low detection limit of 80 nM ATP in buffer solution. Moreover, due to the additive fluorescence lifetime of excimer induced by γ-cyclodextrin, time-resolved measurements could be conveniently used to detect as low as 0.5 μM ATP in blood serum quantitatively.
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Affiliation(s)
- Fen Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China; Hubei Key Laboratory of Mine Environmental Pollution Control & Remediation, Environmental Science and Engineering College, Hubei Polytechnic University, Huangshi 435003, PR China
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190
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A label-free DNA hairpin biosensor for colorimetric detection of target with suitable functional DNA partners. Biosens Bioelectron 2013; 49:236-42. [PMID: 23770395 DOI: 10.1016/j.bios.2013.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/05/2013] [Accepted: 05/19/2013] [Indexed: 01/25/2023]
Abstract
The combination of aptamer and peroxidase-mimicking DNAzyme within a hairpin structure can form a functional DNA probe. The activities of both aptamer (as biorecognition element) and DNAzyme (as signal amplification element) are blocked via base pairing in the hairpin structure. The presence of target triggers the opening of the hairpin to form target/aptamer complex and releases G-quadruplex sequence which can generate amplified colorimetric signals. In this work, we elaborated a universal and simple procedure to design an efficient and sensitive hairpin probe with suitable functional DNA partners. A fill-in-the-blank process was developed for sequence design, and two key points including the pretreatment of the hairpin probe and the selection of suitable signal transducer sequence were proved to enhance the detection sensitivity. Cocaine was chosen as a model target for a proof of concept. A series of hairpins with different numbers of base pairs in the stem region were prepared. Hairpin-C10 with ten base pairs was screened out and a lowest detectable cocaine concentration of 5 μM by colorimetry was obtained. The proposed functional DNA hairpin showed good selectivity and satisfactory analysis in spiked biologic fluid. The whole "mix-and-measure" detection based on DNA hairpin without the need of immobilization and labeling was indicated to be time and labor saving. The strategy has potential to be transplanted into more smart hairpins toward other targets for general application in bioanalytical chemistry.
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191
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He X, Li Z, Jia X, Wang K, Yin J. A highly selective sandwich-type FRET assay for ATP detection based on silica coated photon upconverting nanoparticles and split aptamer. Talanta 2013; 111:105-10. [PMID: 23622532 DOI: 10.1016/j.talanta.2013.02.050] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 02/07/2023]
Abstract
In this paper, we report a highly selective sandwich-type fluorescence resonance energy transfer (FRET) assay for ATP detection by combining the unique optical properties of silica coated photon upconverting NaYF4:Yb(3+), Er(3+) nanoparticles (Si@UCNPs) with the high specific recognition ability of ATP aptamer. In the protocol, a single aptamer of ATP was split into two fragments. One of which was covalently attached to the Si@UCNPs at the 5' end, and the other was labeled with Black Hole Quencher-1 (BHQ1) at the 3' end. In the presence of ATP, the two fragments bound ATP with high affinity to form the sandwich complexes on the surface of Si@UCNPs. ATP induced association of the two fragments, thus bringing the Si@UCNPs and BHQ1 into close proximity. Under the illumination of 980 nm laser, energy transfer took place between the Si@UCNPs as the donor and BHQ1 as the acceptor, creating an optical "sandwich-type" assay for ATP detection. By monitoring the fluorescence change of the Si@UCNPs at 550 nm, the presence of the ATP could be quantitatively detected with a detection limit of 1.70 μM. The linear response range was 2 μM-16 μM. The background of this assay was ignorable because the fluorescence intensity of Si@UCNPs at 550 nm was not changed in the absence of ATP. This assay was also able to discriminate ATP from its analogs.
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Affiliation(s)
- Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of biology, College of Chemistry & Chemical Engineering, Hunan University, Changsha 410082, PR China
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192
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Nakano S, Fukuda M, Tamura T, Sakaguchi R, Nakata E, Morii T. Simultaneous detection of ATP and GTP by covalently linked fluorescent ribonucleopeptide sensors. J Am Chem Soc 2013; 135:3465-73. [PMID: 23373863 DOI: 10.1021/ja3097652] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A noncovalent RNA complex embedding an aptamer function and a fluorophore-labeled peptide affords a fluorescent ribonucleopeptide (RNP) framework for constructing fluorescent sensors. By taking an advantage of the noncovalent properties of the RNP complex, the ligand-binding and fluorescence characteristics of the fluorescent RNP can be independently tuned by taking advantage of the nature of the RNA and peptide subunits, respectively. Fluorescent sensors tailored for given measurement conditions, such as a detection wavelength and a detection concentration range for a ligand of interest can be easily identified by screening of fluorescent RNP libraries. The noncovalent configuration of a RNP becomes a disadvantage when the sensor is to be utilized at very low concentrations or when multiple sensors are applied to the same solution. Here, we report a strategy to convert a fluorescent RNP sensor in the noncovalent configuration into a covalently linked stable fluorescent RNP sensor. This covalently linked fluorescent RNP sensor enabled ligand detection at a low sensor concentration, even in cell extracts. Furthermore, application of both ATP and GTP sensors enabled simultaneous detection of ATP and GTP by monitoring each wavelength corresponding to the respective sensor. Importantly, when a fluorescein-modified ATP sensor and a pyrene-modified GTP sensor were co-incubated in the same solution, the ATP sensor responded at 535 nm only to changes in the concentration of ATP, whereas the GTP sensor detected GTP at 390 nm without any effect on the ATP sensor. Finally, simultaneous monitoring by these sensors enabled real-time measurement of adenosine deaminase enzyme reactions.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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193
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Wang F, Liu X, Willner I. Integration of photoswitchable proteins, photosynthetic reaction centers and semiconductor/biomolecule hybrids with electrode supports for optobioelectronic applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:349-377. [PMID: 22933337 DOI: 10.1002/adma.201201772] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Indexed: 06/01/2023]
Abstract
Light-triggered biological processes provide the principles for the development of man-made optobioelectronic systems. This Review addresses three recently developed topics in the area of optobioelectronics, while addressing the potential applications of these systems. The topics discussed include: (i) the reversible photoswitching of the bioelectrocatalytic functions of redox proteins by the modification of proteins with photoisomerizable units or by the integration of proteins with photoisomerizable environments; (ii) the integration of natural photosynthetic reaction centers with electrodes and the construction of photobioelectrochemical cells and photobiofuel cells; and (iii) the synthesis of biomolecule/semiconductor quantum dots hybrid systems and their immobilization on electrodes to yield photobioelectrochemical and photobiofuel cell elements. The fundamental challenge in the tailoring of optobioelectronic systems is the development of means to electrically contact photoactive biomolecular assemblies with the electrode supports. Different methods to establish electrical communication between the photoactive biomolecular assemblies and electrodes are discussed. These include the nanoscale engineering of the biomolecular nanostructures on surfaces, the development of photoactive molecular wires and the coupling of photoinduced electron transfer reactions with the redox functions of proteins. The different possible applications of optobioelectronic systems are discussed, including their use as photosensors, the design of biosensors, and the construction of solar energy conversion and storage systems.
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Affiliation(s)
- Fuan Wang
- Institute of Chemistry, Center of Nanoscience and Nanotechnology, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Nie J, Deng Y, Deng QP, Zhang DW, Zhou YL, Zhang XX. A self-assemble aptamer fragment/target complex based high-throughput colorimetric aptasensor using enzyme linked aptamer assay. Talanta 2012; 106:309-14. [PMID: 23598133 DOI: 10.1016/j.talanta.2012.11.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/01/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
Enzyme linked aptamer assay (ELAA) uses an aptamer as recognition element and enzyme as signal readout element for establishing different kinds of aptasensors. We reported herein a high-throughput colorimetric aptasensor based on ELAA only requiring a single aptamer sequence for cocaine detection. An anti-cocaine aptamer was cleaved into two fragments, one of which was immobilized on a DNA-BIND 96-well plate via 5'-labeled primary amine and the other one was biotin labeled. The presence of two aptamer fragments and the target molecule led to the formation of aptamer fragments/target complexes. Streptavidin-horseradish peroxidase (SA-HRP) was used to react with biotin in order to obtain quantitative signals. A linear response towards cocaine concentration in the range of 5-200 μM and a detection limit down to 2.8 μM (S/N=3) were achieved. The specificity and application in real sample were validated. Furthermore, a verification test of thrombin detection in the same strategy illustrated its feasibility for not only small molecule but also biomacromolecule. With the advantage of high-throughput, easy operation, high specificity, the colorimetric assay based on ELAA requiring a single aptamer sequence opens up a new approach for detecting different kinds of targets via specific affinity recognition among target and suitably cleaved aptamer fragments.
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Affiliation(s)
- Ji Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Biochemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
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196
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A universal and label-free aptasensor for fluorescent detection of ATP and thrombin based on SYBR Green I dye. Biosens Bioelectron 2012. [PMID: 23202351 DOI: 10.1016/j.bios.2012.10.064] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A facile and universal aptamer-based label-free approach for selective and sensitive fluorescence detection of proteins and small biomolecules by using the SYBR Green I (SGI) dye is developed. This robust versatile biosensing strategy relies on fluorescence turn-off changes of SGI, resulting from target-induced structure switching of aptamers. Upon binding with the targets, the aptamers dissociate from the respective cDNA/aptamer duplexes, leading to the release of the dsDNA-intercalated SGI into solution and the quenching of the corresponding fluorescence intensities. Such target-induced conformational changes and release of aptamers from the DNA duplexes essentially lead to the change in the fluorescence signal of the SGI and thus constitute the mechanism of our aptamer-based label-free fluorescence biosensor for specific target analyses. Under optimized conditions, our method exhibits high sensitivity and selectivity for the quantification of ATP and thrombin with low detection limits (23.4 nM and 1.1 nM, respectively). Compared with previous reported methods for aptamer-based detection of ATP and thrombin, this label-free approach is selective, simple, convenient and cost-efficient without any chemical labeling of the probe or the target. Therefore, the present strategy could be easily applicable to biosensors that target a wide range of biomolecules.
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197
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Li B, Ellington* AD. Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Aptamers are single-stranded nucleic acids that can be selected in vitro with special folding structures to bind to many different small-molecule, protein, and cellular targets. Over the past two decades, aptamers have become novel promising recognition elements for the fabrication of biosensors. These ‘aptasensors’ have several advantages over antibodies in that they are relatively easy to synthesise or modify in vitro, and can be appended with linkers and reporters for adaptation to various sensing strategies. In this chapter, we introduce the various electrochemical techniques that can be used as powerful readout methods for aptasensors, providing a brief introduction to aptamers and related electrochemical techniques, and then a detailed description of various branches within the field, including labelled strategies, unlabelled strategies, and enzyme-amplified strategies. For each type of approach, several basic and improved design principles will be addressed. It is hoped that, through this discussion, readers will get a sense of how several variables (aptamers, targets and redox reporters) are successfully combined with electrochemical techniques in order to produce a series of sensing platforms with high selectivity and sensitivity.
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Affiliation(s)
- Bingling Li
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
| | - Andrew D. Ellington*
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
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198
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Niu S, Lou X, Jiang Y, Lin J. A Novel Fluorescence Sensor for Cocaine with Signal Amplification through Cycling Exo-Cleaving with a Hairpin Probe. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.677972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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199
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Mei H, Bing T, Yang X, Qi C, Chang T, Liu X, Cao Z, Shangguan D. Functional-group specific aptamers indirectly recognizing compounds with alkyl amino group. Anal Chem 2012; 84:7323-9. [PMID: 22881428 DOI: 10.1021/ac300281u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Aptamers are usually generated against a specific molecule. Their high selectivity makes them only suitable for studying specific targets. Since it is nearly impossible to generate aptamers for every molecule, it can be of great interest to select aptamers recognizing a common feature of a group of molecules in many applications. In this paper, we describe the selection of aptamers for indirect recognition of alkyl amino groups. Because amino groups are small and positive charged, we introduced a protection group, p-nitrobenzene sulfonyl (p-nosyl) to convert them into a form suitable for aptamer selection. Taking N(ε)-p-nosyl-L-lysine (PSL) as a target, we obtained a group of aptamers using the SELEX technique. Two optimized aptamers, M6b-M14 and M13a exhibit strong affinity to PSL with the K(d) values in the range of 2-5 μM. They also show strong affinity to other compounds containing p-nosyl-protected amino groups except those also possessing an α-carboxyl group. Both aptamers adopt an antiparallel G-quadruplex structure when binding to targets. An aptamer beacon based on M6b-M14 showed good selectivity toward the reaction mixture of p-nosyl-Cl and alkyl amino compounds, and could recognize lysine from amino acid mixtures indirectly, suggesting that aptamers against a common moiety of a certain type of molecules can potentially lead to many new applications. Through this study, we have demonstrated the ability to select aptamers for a specific part of an organic compound, and the chemical conversion approach may prove to be valuable for aptamer selection against molecules that are generally difficult for SELEX.
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Affiliation(s)
- Hongcheng Mei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Chinese Academy of Sciences, Beijing, 100190, China
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200
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Zhu Z, Ravelet C, Perrier S, Guieu V, Fiore E, Peyrin E. Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules. Anal Chem 2012; 84:7203-11. [PMID: 22793528 DOI: 10.1021/ac301552e] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.
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Affiliation(s)
- Zhenyu Zhu
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
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