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Cao S, Zhao H, Chen K, Zhou F, Lan M. An electrochemical aptasensor based on multi-walled carbon nanotubes loaded with PtCu nanoparticles as signal label for ultrasensitive detection of adenosine. Anal Chim Acta 2023; 1260:341212. [PMID: 37121659 DOI: 10.1016/j.aca.2023.341212] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023]
Abstract
Adenosine, as an endogenous nucleoside modulator, plays an important role in heart rate regulation, neurotransmission, and control of the respiratory system and thus it is significantly important to realize its sensitive detection. Herein, a highly sensitive electrochemical aptasensor for adenosine detection was proposed by using multi-walled carbon nanotubes (MWCNTs) as support matrix loading PtCu nanoparticles (PtCu-MWCNTs) to amplify signal. On one hand, disposable screen-printing gold electrodes (SPGEs) were used as superb sensing base to ensure the stable connection of aptamers 1 (ssDNA1). On the other hand, the PtCu-MWCNTs complex was synthesized through a one-pot method, which not only can precisely control the proportion of metal mass in the product but also exhibited superior electrocatalytic activity towards H2O2. The recognition reactions were achieved by stepwise incubation of ssDNA1, ssDNA2-PtCu-MWCNTs (denoted as ssDNA2-label), and adenosine on the SPGEs. As a result, the constructed electrochemical aptasensor exhibited a wide linear range from 10 nM to 1.0 μM with a low detection limit of 1.0 nM (S/N = 3) for adenosine detection. The aptasensor also successfully realized the adenosine detection in human serum samples, which means that the proposed aptasensor holds a potential application in point-of-care detection.
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Affiliation(s)
- Shida Cao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Kaicha Chen
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Fangfang Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China; Research Center of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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2
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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3
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Liu D, Wang J, Wu L, Huang Y, Zhang Y, Zhu M, Wang Y, Zhu Z, Yang C. Trends in miniaturized biosensors for point-of-care testing. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115701] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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4
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Akter R, Jeong B, Lee YM, Choi JS, Rahman MA. Femtomolar detection of cardiac troponin I using a novel label-free and reagent-free dendrimer enhanced impedimetric immunosensor. Biosens Bioelectron 2017; 91:637-643. [DOI: 10.1016/j.bios.2017.01.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 01/02/2023]
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5
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MicroRNA-mediated signal amplification coupled with GNP/dendrimers on a mass-sensitive biosensor and its applications in intracellular microRNA quantification. Biosens Bioelectron 2016; 85:897-902. [DOI: 10.1016/j.bios.2016.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 12/14/2022]
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6
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Felletti M, Hartig JS. Ligand-dependent ribozymes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27687155 DOI: 10.1002/wrna.1395] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 12/20/2022]
Abstract
The discovery of catalytic RNA (ribozymes) more than 30 years ago significantly widened the horizon of RNA-based functions in natural systems. Similarly to the activity of protein enzymes that are often modulated by the presence of an interaction partner, some examples of naturally occurring ribozymes are influenced by ligands that can either act as cofactors or allosteric modulators. Recent discoveries of new and widespread ribozyme motifs in many different genetic contexts point toward the existence of further ligand-dependent RNA catalysts. In addition to the presence of ligand-dependent ribozymes in nature, researchers have engineered ligand dependency into natural and artificial ribozymes. Because RNA functions can often be assembled in a truly modular way, many different systems have been obtained utilizing different ligand-sensing domains and ribozyme activities in diverse applications. We summarize the occurrence of ligand-dependent ribozymes in nature and the many examples realized by researchers that engineered ligand-dependent catalytic RNA motifs. We will also highlight methods for obtaining ligand dependency as well as discuss the many interesting applications of ligand-controlled catalytic RNAs. WIREs RNA 2017, 8:e1395. doi: 10.1002/wrna.1395 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michele Felletti
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany
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7
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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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8
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Akter R, Jeong B, Rahman MA. Stimulated mass enhancement strategy-based highly sensitive detection of a protein in serum using quartz crystal microbalance technique. Analyst 2015; 140:995-8. [DOI: 10.1039/c4an01555j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A quartz crystal microbalance immunosensor is described for highly sensitive detection of interleukin-6 in serum using a magnetic bead-supported bienzyme-catalyzed stimulated mass enhancement strategy.
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Affiliation(s)
- Rashida Akter
- Graduate School of Analytical Science and Technology
- Chungnam National University
- South Korea
| | - Bongjin Jeong
- Graduate School of Analytical Science and Technology
- Chungnam National University
- South Korea
| | - Md. Aminur Rahman
- Graduate School of Analytical Science and Technology
- Chungnam National University
- South Korea
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9
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Huang Y, Zhang Q, Liu G, Zhao R. A continuous-flow mass biosensor for the real-time dynamic analysis of protease inhibition. Chem Commun (Camb) 2015; 51:6601-4. [DOI: 10.1039/c5cc00885a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A flow injection analysis–quartz crystal microbalance (FIA–QCM) biosensor system was introduced for probing the dynamic interactions during protease inhibition.
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Affiliation(s)
- Yanyan Huang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Qundan Zhang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Guoquan Liu
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Rui Zhao
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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10
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Frommer J, Appel B, Müller S. Ribozymes that can be regulated by external stimuli. Curr Opin Biotechnol 2014; 31:35-41. [PMID: 25146171 DOI: 10.1016/j.copbio.2014.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022]
Abstract
Ribozymes have been known for about 30 years, and nowadays are understood well enough to be turned into useful tools for a number of applications in vitro and in vivo. Allosteric ribozymes switch on and off their activity in response to a specific chemical (ligand) or physical (temperature, light) signal. The possibility of controlling ribozyme activity by external stimuli is of particular relevance for applications in different fields, such as environmental and medicinal diagnostics, molecular computing, control of gene expression and others. Herein, we review recent advances and describe selected examples of addressable ribozymes.
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Affiliation(s)
- Jennifer Frommer
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Bettina Appel
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany
| | - Sabine Müller
- Ernst Moritz Arndt University Greifswald, Institute for Biochemistry, Felix Hausdorff Str. 4, D-17487 Greifswald, Germany.
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11
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Sett A, Das S, Bora U. Functional nucleic-acid-based sensors for environmental monitoring. Appl Biochem Biotechnol 2014; 174:1073-91. [PMID: 24903959 DOI: 10.1007/s12010-014-0990-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/19/2014] [Indexed: 01/16/2023]
Abstract
Efforts to replace conventional chromatographic methods for environmental monitoring with cheaper and easy to use biosensors for precise detection and estimation of hazardous environmental toxicants, water or air borne pathogens as well as various other chemicals and biologics are gaining momentum. Out of the various types of biosensors classified according to their bio-recognition principle, nucleic-acid-based sensors have shown high potential in terms of cost, sensitivity, and specificity. The discovery of catalytic activities of RNA (ribozymes) and DNA (DNAzymes) which could be triggered by divalent metallic ions paved the way for their extensive use in detection of heavy metal contaminants in environment. This was followed with the invention of small oligonucleotide sequences called aptamers which can fold into specific 3D conformation under suitable conditions after binding to target molecules. Due to their high affinity, specificity, reusability, stability, and non-immunogenicity to vast array of targets like small and macromolecules from organic, inorganic, and biological origin, they can often be exploited as sensors in industrial waste management, pollution control, and environmental toxicology. Further, rational combination of the catalytic activity of DNAzymes and RNAzymes along with the sequence-specific binding ability of aptamers have given rise to the most advanced form of functional nucleic-acid-based sensors called aptazymes. Functional nucleic-acid-based sensors (FNASs) can be conjugated with fluorescent molecules, metallic nanoparticles, or quantum dots to aid in rapid detection of a variety of target molecules by target-induced structure switch (TISS) mode. Although intensive research is being carried out for further improvements of FNAs as sensors, challenges remain in integrating such bio-recognition element with advanced transduction platform to enable its use as a networked analytical system for tailor made analysis of environmental monitoring.
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Affiliation(s)
- Arghya Sett
- Bioengineering Research Laboratory, Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
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12
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Sensitivity enhancement of an electrochemical immunosensor through the electrocatalysis of magnetic bead-supported non-enzymatic labels. Biosens Bioelectron 2014; 54:351-7. [DOI: 10.1016/j.bios.2013.10.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 01/17/2023]
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13
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Dong ZM, Zhao GC. A theophylline quartz crystal microbalance biosensor based on recognition of RNA aptamer and amplification of signal. Analyst 2014; 138:2456-62. [PMID: 23467569 DOI: 10.1039/c3an36775d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A quartz crystal microbalance (QCM) biosensor for theophylline was developed by recognition of RNA aptamer and gold nanoparticle amplification technique. Firstly, a designed small single-stranded RNA, RNA1, was immobilized onto the QCM electrode through a thiol linker. Then, the complementary stranded RNA2, which can combine with RNA1 to form a double-stranded RNA with a recognition unit of theophylline, could be self-assembled on the QCM electrode surface through a hybrid reaction in the presence of theophylline. The recognition process could cause a frequency change of QCM to give the signal related to theophylline. When RNA2 was tethered to gold nanoparticles, the signal could be amplified to further enhance the sensitivity of the designed sensor. Under the optimal conditions, the QCM-based biosensor showed excellent sensitivity (limit of detection, 8.2 nM) and specificity with a dissociation constant of Kd = 5.26 × 10(-7) M. The sensor can be used to quantitatively detect theophylline in serum, suggesting that it can be applied in complex biological samples.
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Affiliation(s)
- Zong-Mu Dong
- Anhui key laboratory of Chem-Biosensing, School of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
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14
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Li X, Song J, Wang Y, Cheng T. Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease. Anal Chim Acta 2013; 797:95-101. [DOI: 10.1016/j.aca.2013.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 01/10/2023]
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15
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Carter JR, Balaraman V, Kucharski CA, Fraser TS, Fraser MJ. A novel dengue virus detection method that couples DNAzyme and gold nanoparticle approaches. Virol J 2013; 10:201. [PMID: 23809208 PMCID: PMC3765938 DOI: 10.1186/1743-422x-10-201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/08/2013] [Indexed: 11/15/2022] Open
Abstract
Background Recent epidemics of dengue viruses (DENV) coupled with new outbreaks on the horizon have renewed the demand for novel detection methods that have the ability to identify this viral pathogen prior to the manifestation of symptoms. The ability to detect DENV in a timely manner is essential for rapid recovery from disease symptoms. A modified lab-derived 10-23 DNAzyme tethered to gold nanoparticles provides a powerful tool for the detection of viruses, such as DENV. Results We examined the effectiveness of coupling DNAzyme (DDZ) activation to the salt-induced aggregation of gold nanoparticles (AuNP) to detect dengue virus (DENV) progeny in mosquito cells. A DNAzyme was designed to recognize the 5’ cyclization sequence (5’ CS) that is conserved among all DENV, and conjugated to AuNPs. DDZ-AuNP has demonstrated the ability to detect the genomic RNA of our model dengue strain, DENV-2 NGC, isolated from infected Aedes albopictus C6/36 cells. These targeting events lead to the rapid aggregation of AuNPs, resulting in a red to clear color transition of the reaction mixes, and thus positive detection of the DENV RNA genome. The inclusion of SDS in the reaction mixture permitted the detection of DENV directly from cell culture supernatants without additional sample processing. Specificity assays demonstrated detection is DENV-specific, while sensitivity assays confirm detection at levels of 1 × 101 TCID50 units. These results demonstrate DDZ-AuNP effectively detects DENV genomes in a sequence specific manner and at concentrations that are practical for field use. Conclusions We have developed an effective detection assay using DNAzyme catalysis coupled with AuNP aggregation for the detection of DENV genomes in a sequence specific manner. Full development of our novel DDZ-AuNP detection method will provide a practical, rapid, and low cost alternative for the detection of DENV in mosquito cells and tissues, and possibly infected patient serum, in a matter of minutes with little to no specialized training required.
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Affiliation(s)
- James R Carter
- Department of Biological Sciences, Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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16
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Noonan PS, Roberts RH, Schwartz DK. Liquid Crystal Reorientation Induced by Aptamer Conformational Changes. J Am Chem Soc 2013; 135:5183-9. [DOI: 10.1021/ja400619k] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Patrick S. Noonan
- Department of Chemical
and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0424,
United States
| | - Richard H. Roberts
- Department of Chemical
and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0424,
United States
| | - Daniel K. Schwartz
- Department of Chemical
and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309-0424,
United States
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17
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Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization. Anal Chim Acta 2012; 735:114-20. [DOI: 10.1016/j.aca.2012.05.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/12/2012] [Accepted: 05/17/2012] [Indexed: 01/08/2023]
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18
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Cheng CI, Chang YP, Chu YH. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications. Chem Soc Rev 2012; 41:1947-71. [DOI: 10.1039/c1cs15168a] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Lee J, Choi YS, Lee Y, Lee HJ, Lee JN, Kim SK, Han KY, Cho EC, Park JC, Lee SS. Sensitive and Simultaneous Detection of Cardiac Markers in Human Serum Using Surface Acoustic Wave Immunosensor. Anal Chem 2011; 83:8629-35. [DOI: 10.1021/ac2020849] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonhyung Lee
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Youn-Suk Choi
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yeolho Lee
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Hun Joo Lee
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
- Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-dong, Mapo-gu, Seoul, Republic of Korea
| | - Jung Nam Lee
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sang Kyu Kim
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Kyung Yeon Han
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Eun Chol Cho
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jae Chan Park
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Soo Suk Lee
- Bio Lab, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., San #14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Republic of Korea
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20
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Abstract
Aptamers are DNA or RNA oligonucleotides that can bind with high affinity and specificity to a wide range of targets such as proteins, metal ions or pathogenic microorganisms. Soluble aptamers and aptazymes have been used as sensing elements for developing homogeneous assays in a solution phase, the whole sensing process being carried out in a homogeneous solution. Contrary to most conventional heterogeneous assays that are time-consuming and labor-intensive, aptamer-based homogeneous assays are simple, easy-to-perform, rapid and do not require immobilization nor washing steps. To our knowledge, this review is the first entirely dedicated to aptamer-based homogeneous assays. Optical detection appears as the most developed technique. Colorimetry represents the simplest sensing mode that occupies a very important position among aptamer-based assays, involving gold nanoparticle aggregation (with unmodified or aptamer-modified gold NPs), the formation of HRP-mimicking DNAzyme with hemin, dye displacement or interactions with a cationic polymer. Fluorescence that is highly sensitive offers the most developed detection mode. Aptamers can be labeled or not, to give rise to turn-on or usually less sensitive turn-off fluorescent assays. Newly reported and thus less developed non-conventional magnetic resonance imaging (MRI) and electrochemistry also recently appeared in the literature, thrombin still remains the main detected target. Homogeneous assays based on aptazyme, an aptamer sequence connected to a known ribozyme motif, are also described in this review, involving optical detection, by colorimetry or fluorescence.
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Affiliation(s)
- Audrey Sassolas
- CNRS, UMR 5246, ICBMS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Génie Enzymatique, Membranes Biomimétiques et Assemblages Supramoléculaires (GEMBAS), Université Lyon 1, Bât CPE, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622, France
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21
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North SH, Lock EH, Taitt CR, Walton SG. Critical aspects of biointerface design and their impact on biosensor development. Anal Bioanal Chem 2010; 397:925-33. [PMID: 20349179 DOI: 10.1007/s00216-010-3637-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/04/2010] [Accepted: 03/07/2010] [Indexed: 11/29/2022]
Abstract
The stable integration of a biological recognition element on a transducing substrate surface is the single most important step in the creation of a high-functioning sensor surface. The key factors affecting biotic and abiotic functionalities at the biointerface are both chemical and physical. Understanding the interactions between biomolecules and surfaces, and their emergent complexity, is critical for biointerface implementation for sensing applications. In this overview, we highlight materials and methods typically used for biosensor development. Particular emphasis has been given to the experimental evaluation of biointerfacial properties and functionality. Promising research directions for application of biointerfaces to biosensing are suggested.
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Affiliation(s)
- Stella H North
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
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22
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Ogawa A. Biofunction-assisted sensors based on a new method for converting aptazyme activity into reporter protein expression with high efficiency in wheat germ extract. Chembiochem 2010; 10:2465-8. [PMID: 19750532 DOI: 10.1002/cbic.200900497] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Atsushi Ogawa
- Senior Research Fellow Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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23
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Zhao Q, de Zoysa RSS, Wang D, Jayawardhana DA, Guan X. Real-time monitoring of peptide cleavage using a nanopore probe. J Am Chem Soc 2009; 131:6324-5. [PMID: 19368382 DOI: 10.1021/ja9004893] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we report a rapid, label-free method for monitoring peptide cleavage. Monitoring peptide translocation through an engineered ion channel in the absence and the presence of an enzyme allowed quantitative chemical kinetics information on enzymatic processes to be obtained. In addition to its potential application in disease diagnostics and drug discovery, this peptide/protein cleavage approach is envisioned for further development as a novel rapid, label-free protein sequencing technique.
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Affiliation(s)
- Qitao Zhao
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-0065, USA
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24
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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25
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Ogawa A, Maeda M. A novel label-free biosensor using an aptazyme-suppressor-tRNA conjugate and an amber mutated reporter gene. Chembiochem 2009; 9:2204-8. [PMID: 18756550 DOI: 10.1002/cbic.200800294] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Atsushi Ogawa
- Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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26
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Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:241-64. [PMID: 20636061 DOI: 10.1146/annurev.anchem.1.031207.112851] [Citation(s) in RCA: 577] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.
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Affiliation(s)
- Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA.
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27
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Ogawa A, Maeda M. Simple and rapid colorimetric detection of cofactors of aptazymes using noncrosslinking gold nanoparticle aggregation. Bioorg Med Chem Lett 2008; 18:6517-20. [DOI: 10.1016/j.bmcl.2008.10.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 09/16/2008] [Accepted: 10/10/2008] [Indexed: 01/04/2023]
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28
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Lu N, Shao C, Deng Z. Rational design of an optical adenosine sensor by conjugating a DNA aptamer with split DNAzyme halves. Chem Commun (Camb) 2008:6161-3. [PMID: 19082106 DOI: 10.1039/b810812a] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Split halves of a hemin-binding DNAzyme have been assembled with an anti-adenosine aptamer to build a homogeneous allosteric sensor for adenosine with high selectivity and sensitivity.
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Affiliation(s)
- Na Lu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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29
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Shen L, Chen Z, Li Y, He S, Xie S, Xu X, Liang Z, Meng X, Li Q, Zhu Z, Li M, Le XC, Shao Y. Electrochemical DNAzyme Sensor for Lead Based on Amplification of DNA−Au Bio-Bar Codes. Anal Chem 2008; 80:6323-8. [DOI: 10.1021/ac800601y] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Shen
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhong Chen
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yihan Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Shali He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Shubao Xie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xiaodong Xu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhongwei Liang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xin Meng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Qing Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Zhiwei Zhu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Meixian Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yuanhua Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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30
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Ogawa A, Maeda M. Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors. Bioorg Med Chem Lett 2007; 17:3156-60. [PMID: 17391960 DOI: 10.1016/j.bmcl.2007.03.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/07/2007] [Accepted: 03/10/2007] [Indexed: 11/20/2022]
Abstract
We constructed a label-free and detector-free aptazyme-based riboswitch sensor for detecting the cofactor of the aptazyme. This riboswitch, which usually suppresses the gene expression with its anti-RBS sequence bound to the RBS of its own mRNA (OFF), activates the translation only when a cofactor is added to release the anti-RBS sequence from itself as a result of cofactor-induced self-cleavage by the aptazyme (ON). The rationally optimized one with beta-galactosidase as a reporter gene enabled us to detect the cofactor of the aptazyme visibly with high ON/OFF efficiency.
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Affiliation(s)
- Atsushi Ogawa
- Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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