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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer–Cyanine Complexes as Generic Colorimetric Small‐Molecule Sensors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112305] [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]
Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Konstantin V. Bukhryakov
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anthony P. DeCaprio
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer-Cyanine Complexes as Generic Colorimetric Small-Molecule Sensors. Angew Chem Int Ed Engl 2021; 61:e202112305. [PMID: 34706127 DOI: 10.1002/anie.202112305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 12/31/2022]
Abstract
Aptamers are promising biorecognition elements for sensors. However, aptamer-based assays often lack the requisite levels of sensitivity and/or selectivity because they typically employ structure-switching aptamers with attenuated affinity and/or utilize reporters that require aptamer labeling or which are susceptible to false positives. Dye-displacement assays offer a label-free, sensitive means for overcoming these issues, wherein target binding liberates a dye that is complexed with the aptamer, producing an optical readout. However, broad utilization of these assays has been limited. Here, we demonstrate a rational approach to develop colorimetric cyanine dye-displacement assays that can be broadly applied to DNA aptamers regardless of their structure, sequence, affinity, or the physicochemical properties of their targets. Our approach should accelerate the development of mix-and-measure assays that could be applied for diverse analytical applications.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Konstantin V Bukhryakov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anthony P DeCaprio
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
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Zejli H, Goud KY, Marty JL. An electrochemical aptasensor based on polythiophene-3-carboxylic acid assisted methylene blue for aflatoxin B1 detection. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Razmi N, Baradaran B, Hejazi M, Hasanzadeh M, Mosafer J, Mokhtarzadeh A, de la Guardia M. Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor. Biosens Bioelectron 2018; 113:58-71. [PMID: 29729560 DOI: 10.1016/j.bios.2018.04.048] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/16/2018] [Accepted: 04/20/2018] [Indexed: 01/13/2023]
Abstract
Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional methods for PDGF-BB detection, requiring high-cost and complicated instrumentation, take too much time and offer deficient sensitivity and selectivity, which restrict their usage in real applications. Hence, it is essential to design and build enhanced systems and platforms for the recognition and quantification of protein biomarkers. In the past few years, biosensors especially aptasensors have been received noticeable attention for the detection of PDGF-BB owing to their high sensitivity, selectivity, accuracy, fast response, and low cost. Since the role and importance of developing aptasensors in cancer diagnosis is undeniable. In this review, optical and electrochemical aptasensors, which have been applied by many researchers for PDGF-BB cancer biomarker detection, have been mentioned and merits and demerits of them have been explained and compared. Efforts related to design and development of aptamer-based biosensors using nanoparticles for sensitive and selective detection of PDGF-BB have been reviewed considering: Aptamer importance as recognition elements, principal, application and the recent improvements and developments of aptamer based optical and electrochemical methods. In addition, commercial biosensors and future perspectives for rapid and on-site detection of PDGF-BB have been summarized.
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Affiliation(s)
- Nasrin Razmi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz 51664 Iran
| | - Jafar Mosafer
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran.
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
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Perrier S, Guieu V, Chovelon B, Ravelet C, Peyrin E. Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms. Anal Chem 2018. [PMID: 29513518 DOI: 10.1021/acs.analchem.7b04593] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.
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Affiliation(s)
- Sandrine Perrier
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Valérie Guieu
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Benoit Chovelon
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France.,Département de Biochimie, Toxicologie et Pharmacologie , CHU de Grenoble Site Nord-Institut de Biologie et de Pathologie , F-38041 Grenoble , France
| | - Corinne Ravelet
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Eric Peyrin
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. A lifetime-sensitive fluorescence anisotropy probe for DNA-based bioassays: The case of SYBR Green. Biosens Bioelectron 2016; 90:140-145. [PMID: 27886600 DOI: 10.1016/j.bios.2016.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/01/2016] [Accepted: 11/20/2016] [Indexed: 12/12/2022]
Abstract
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer. On the basis of ligand-induced changes in the molar fractions of bound and free forms of SG, the approach provides an unprecedented means for the FA monitoring of the ligand binding to short DNA molecules, allowing the elaboration of a variety of intercalator displacement assays and label-free biosensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), ligand types (ion, small organic molecule and protein) and binding modes (intercalation, minor groove, allosteric switch). These findings open up promising avenues in the design of a new generation of FA assays.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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Xu H, Liang S, Zhu X, Wu X, Dong Y, Wu H, Zhang W, Chi Y. Enhanced electrogenerated chemiluminescence behavior of C 3N 4 QDs@ C 3N 4 nanosheet and its signal-on aptasensing for platelet derived growth factor. Biosens Bioelectron 2016; 92:695-701. [PMID: 27829561 DOI: 10.1016/j.bios.2016.10.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 01/27/2023]
Abstract
A novel g-C3N4 nanosheets embedded with C3N4 QDs nanocomposites (QD@CNNS) was prepared by simple oxidation using hydrogen peroxide and UV light irradiation. This nanocomposite exhibits more stable and stronger electrochemiluminescent (ECL) behavior compared with CNNS. Coupling this nanocomposite with Fc-labeled aptamer, a signal-on aptasensor for platelet derived growth factor BB (PDGF-BB) is fabricated. Initially, the Fc-labeled aptamer binds onto QD@CNNS via π-π conjugation and electrostatic interaction, quenching ECL emission from QD@CNNS. The introduction of target efficiently recovers the ECL signal by the formation of PDGF-BB/aptamer complex. The ECL intensity is proportion to the concentration of PDGF-BB in the range of 0.02-80nM with a detection limit of 0.013nM. This work demonstrates a simple synthesis method to obtain QD@CNNS with excellent ECL behavior, and opens up the application of g-C3N4 nanocomposite in signal-on aptasensing.
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Affiliation(s)
- Huifeng Xu
- MOE Key Laboratory of Analysis and Detection for Food Safety, State Key Laboratory of Photo catalysis on Energy and Environment, and College of Chemistry, Fuzhou University, Fujian 350108, PR China; Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Shijing Liang
- Department of Environmental Science and Engineering, Fuzhou University, Minhou, Fujian 350108, PR China
| | - Xi Zhu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Xiuqin Wu
- Department of Environmental Science and Engineering, Fuzhou University, Minhou, Fujian 350108, PR China
| | - Yongqiang Dong
- MOE Key Laboratory of Analysis and Detection for Food Safety, State Key Laboratory of Photo catalysis on Energy and Environment, and College of Chemistry, Fuzhou University, Fujian 350108, PR China
| | - Haishan Wu
- MOE Key Laboratory of Analysis and Detection for Food Safety, State Key Laboratory of Photo catalysis on Energy and Environment, and College of Chemistry, Fuzhou University, Fujian 350108, PR China
| | - Wenxia Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Yuwu Chi
- MOE Key Laboratory of Analysis and Detection for Food Safety, State Key Laboratory of Photo catalysis on Energy and Environment, and College of Chemistry, Fuzhou University, Fujian 350108, PR China.
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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Crivianu-Gaita V, Thompson M. Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements. Biosens Bioelectron 2016; 85:32-45. [PMID: 27155114 DOI: 10.1016/j.bios.2016.04.091] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/11/2016] [Accepted: 04/26/2016] [Indexed: 01/14/2023]
Abstract
The choice of biosensing elements is crucial for the development of the optimal biosensor. Three of the most versatile biosensing elements are antibody single-chain Fv fragments (scFv), antibody fragment-antigen binding (Fab') units, and aptamers. This article provides an overview of these three biorecognition elements with respects to their synthesis/engineering, various immobilization techniques, and examples of their use in biosensors. Furthermore, the final section of the review compares and contrasts their characteristics (time/cost of development, ease and variability of immobilization, affinity, stability) illustrating their advantages and disadvantages. Overall, scFv fragments are found to display the highest customizability (i.e. addition of functional groups, immobilizing peptides, etc.) due to recombinant synthesis techniques. If time and cost are an issue in the development of the biosensor, Fab' fragments should be chosen as they are relatively cheap and can be developed quickly from whole antibodies (several days). However, if there are sufficient funds and time is not a factor, aptamers should be utilized as they display the greatest affinity towards their target analytes and are extremely stable (excellent biosensor regenerability).
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Affiliation(s)
| | - Michael Thompson
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
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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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Catanante G, Mishra RK, Hayat A, Marty JL. Sensitive analytical performance of folding based biosensor using methylene blue tagged aptamers. Talanta 2016; 153:138-44. [PMID: 27130100 DOI: 10.1016/j.talanta.2016.03.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/26/2016] [Accepted: 03/02/2016] [Indexed: 11/18/2022]
Abstract
This work demonstrates the development of a folding based electrochemical aptasensor using methylene blue (MB) tagged anti-Ochratoxin A (OTA) aptamers. Different aptamer coupling strategies were tested using Hexamethylenediamine, polyethylene glycol, simple adsorption and diazonium coupling mechanism. The best sensitivity was recorded by oxidation of amines using hexamethylenediamine (HDMA) on screen printed carbon electrode (SPCE). To achieve the direct detection of OTA, aptamer conjugated redox probe was used and detection was demonstrated based on the conformational changes in aptamer structure upon OTA sensing. Signaling in this class of sensors arises from changes in electron transfer efficiency upon target-induced changes in the conformation/flexibility of the aptamer probe. These changes can be readily recorded electrochemically. The developed aptasensor is unique in its own mechanism as redox probe tagged aptamer coupling such as MB has never been tried to immobilize using long carbon chain spacers as, addition of spacers would provide more sensitive detection methods. A good dynamic range 0.01-5ng/ml was obtained for OTA with Limit of detection (LOD) 0.01ng/ml and Limit of quantification (LOQ) of 0.03ng/ml respectively. The good reproducibility was recorded with RSD% of 3.75. The obtained straight line equation was y=0.4035x+0.90311, r=0.9976. We believe that the sensor design guidelines outlined here represents a general strategy for developing new folding-based electrochemical aptasensors. The developed aptasensor was extended to screen cocoa samples for OTA contamination. The cocoa samples were extracted and purified using molecular imprinted polymer (MIP) columns. The aptasensor displayed good recovery values in the range 84-85% thus, exhibited the effectiveness of proposed aptasensor for such complex matrices.
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Affiliation(s)
- Gaëlle Catanante
- Laboratoire B.A.E., Université De Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France
| | - Rupesh K Mishra
- Laboratoire B.A.E., Université De Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France
| | - Akhtar Hayat
- Laboratoire B.A.E., Université De Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology (CIIT), Lahore 54000, Pakistan
| | - Jean-Louis Marty
- Laboratoire B.A.E., Université De Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France
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Wang Y, Li H, Xu D. Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection. Anal Chim Acta 2015; 905:149-55. [PMID: 26755149 DOI: 10.1016/j.aca.2015.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/04/2015] [Accepted: 12/12/2015] [Indexed: 12/26/2022]
Abstract
In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China; School of Environmental Science, Nanjing Xiaozhuang University, China.
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
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Mozioglu E, Gokmen O, Tamerler C, Kocagoz ZT, Akgoz M. Selection of Nucleic Acid Aptamers Specific for Mycobacterium tuberculosis. Appl Biochem Biotechnol 2015; 178:849-64. [PMID: 26541162 DOI: 10.1007/s12010-015-1913-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains to be a major global health problem, with about 9 million new cases and 1.4 million deaths in 2011. For the control of tuberculosis as well as other infectious diseases, WHO recommended "ASSURED" (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free, and Deliverable to the end user) diagnostic tools that can easily be maintained and used in developing countries. Aptamers are promising tools for developing point-of-care diagnostic assays for TB. In this study, ssDNA aptamers that recognize Mycobacterium tuberculosis H37Ra were selected by systematic evolution of ligands by exponential enrichment (SELEX). For this purpose, two different selection protocols, ultrafiltration and centrifugation, were applied. A total of 21 TB specific aptamers were selected. These aptamers exhibited "G-rich" regions on the 3' terminus of the aptamers, including a motif of "TGGGG," "GTGG," or "CTGG." Binding capability of selected aptamers were investigated by quantitative PCR and Mtb36 DNA aptamer was found the most specific aptamer to M. tuberculosis H37Ra. The dissociation constant (K d) of Mtb36 aptamer was calculated as 5.09 ± 1.43 nM in 95% confidence interval. Relative binding ratio of Mtb36 aptamer to M. tuberculosis H37Ra over Mycobacterium bovis and Escherichia coli was also determined about 4 times and 70 times more, respectively. Mtb36 aptamer is highly selective for M. tuberculosis, and it can be used in an aptamer-based biosensor for the detection of M. tuberculosis.
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Affiliation(s)
- Erkan Mozioglu
- Molecular Biology-Biotechnology & Genetics Research Center, Istanbul Technical University, Istanbul, Turkey. .,Bioanalysis Laboratory, TÜBİTAK UME (National Metrology Institute), Kocaeli, Turkey.
| | - Ozgur Gokmen
- Chemistry Department, Gebze Institute of Technology, Kocaeli, Turkey.
| | - Candan Tamerler
- Molecular Biology-Biotechnology & Genetics Research Center, Istanbul Technical University, Istanbul, Turkey. .,Mechanical Engineering and Bioengineering Research Center, University of Kansas, Lawrence, KS, USA.
| | - Zuhtu Tanil Kocagoz
- Department of Microbiology and Clinical Microbiology, Acıbadem University, Istanbul, Turkey. .,Trends in Innovative Biotechnology Organization, Istanbul, Turkey.
| | - Muslum Akgoz
- Bioanalysis Laboratory, TÜBİTAK UME (National Metrology Institute), Kocaeli, Turkey.
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15
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Hu J, Kim J, Easley CJ. Quantifying Aptamer-Protein Binding via Thermofluorimetric Analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:7358-7362. [PMID: 26366207 PMCID: PMC4562029 DOI: 10.1039/c5ay00837a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effective aptamer-based protein assays require coupling to a quantitative reporter of aptamer-protein binding. Typically, this involves a direct optical or electrochemical readout of DNA hybridization or an amplification step coupled to the readout. However, method development is often hampered by the multiplicity of aptamer-target binding mechanisms, which can interfere with the hybridization step. As a simpler and more generalizable readout of aptamer-protein binding, we report that thermofluorimetric analysis (TFA) can be used to quantitatively assay protein levels. Sub-nanomolar detection (0.74 nM) of platelet-derived growth factor (PDGF) with its corresponding aptamer is shown as a test case. In the presence of various DNA intercalating dyes, protein-bound aptamers exhibit a change in fluorescence intensity compared to the intercalated, unbound aptamer. This allows thermal resolution of bound and unbound aptamers using fluorescence melting analysis (-dF/dT curves). Remarkably, the homogeneous optical method allows subtraction of autofluorescence in human serum, giving PDGF detection limits of 1.8 and 10.7 nM in serum diluted 1:7 and 1:3, respectively. We have thus demonstrated that bound and unbound aptamers can be thermally resolved in a homogeneous format using a simple qPCR instrument-even in human serum. The simplicity of this approach provides an important step toward a robust, generalizable readout of aptamer-protein binding.
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Affiliation(s)
- Juan Hu
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Joonyul Kim
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Christopher J. Easley
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
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16
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Schoukroun-Barnes LR, Glaser EP, White RJ. Heterogeneous Electrochemical Aptamer-Based Sensor Surfaces for Controlled Sensor Response. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6563-9. [PMID: 26005758 PMCID: PMC5627764 DOI: 10.1021/acs.langmuir.5b01418] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Structure-switching sensors utilize recognition elements that undergo a conformation change upon target binding that is converted into a quantitative signal. Electrochemical, aptamer-based sensors achieve detection of analytes through a conformation change in an electrode-bound, oligonucleotide aptamer by measuring changes in electron transfer efficiencies. The analytical performance of these sensors is related to the magnitude of the conformation change of the aptamer. The goal of the present work is to develop a general method to predictably tune the analytical performance (sensitivity and linear range) of electrochemical, aptamer-based sensors by utilizing a mixture of rationally designed aptamer sequences that are specific for the same target but with different affinities on the same electrode surface. To demonstrate control over sensor performance, we developed heterogeneous sensors for two representative small molecule targets (adenosine triphosphate and tobramycin). We demonstrate that mixtures of modified sequences can be used to tune the affinity, dynamic range, and sensitivity of the resulting sensors predicted by a bi-Langmuir-type isotherm.
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17
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Lao YH, Phua KKL, Leong KW. Aptamer nanomedicine for cancer therapeutics: barriers and potential for translation. ACS NANO 2015; 9:2235-54. [PMID: 25731717 DOI: 10.1021/nn507494p] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Aptamer nanomedicine, including therapeutic aptamers and aptamer nanocomplexes, is beginning to fulfill its potential in both clinical trials and preclinical studies. Especially in oncology, aptamer nanomedicine may perform better than conventional or antibody-based chemotherapeutics due to specificity compared to the former and stability compared to the latter. Many proof-of-concept studies on applying aptamers to drug delivery, gene therapy, and cancer imaging have shown promising efficacy and impressive safety in vivo toward translation. Yet, there remains ample room for improvement and critical barriers to be addressed. In this review, we will first introduce the recent progress in clinical trials of aptamer nanomedicine, followed by a discussion of the barriers at the design and in vivo application stages. We will then highlight recent advances and engineering strategies proposed to tackle these barriers. Aptamer cancer nanomedicine has the potential to address one of the most important healthcare issues of the society.
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Affiliation(s)
- Yeh-Hsing Lao
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
| | | | - Kam W Leong
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
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18
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Xing YP, Liu C, Zhou XH, Shi HC. Label-free detection of kanamycin based on a G-quadruplex DNA aptamer-based fluorescent intercalator displacement assay. Sci Rep 2015; 5:8125. [PMID: 25634469 PMCID: PMC4311242 DOI: 10.1038/srep08125] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/06/2015] [Indexed: 11/09/2022] Open
Abstract
This work was the first to report that the kanamycin-binding DNA aptamer (5'-TGG GGG TTG AGG CTA AGC CGA-3') can form stable parallel G-quadruplex DNA (G4-DNA) structures by themselves and that this phenomenon can be verified by nondenaturing polyacrylamide gel electrophoresis and circular dichroism spectroscopy. Based on these findings, we developed a novel label-free strategy for kanamycin detection based on the G4-DNA aptamer-based fluorescent intercalator displacement assay with thiazole orange (TO) as the fluorescence probe. In the proposed strategy, TO became strongly fluorescent upon binding to kanamycin-binding G4-DNA. However, the addition of kanamycin caused the displacement of TO from the G4-DNA-TO conjugate, thereby resulting in decreased fluorescent signal, which was inversely related to the kanamycin concentration. The detection limit of the proposed assay decreased to 59 nM with a linear working range of 0.1 μM to 20 μM for kanamycin. The cross-reactivity against six other antibiotics was negligible compared with the response to kanamycin. A satisfactory recovery of kanamycin in milk samples ranged from 80.1% to 98.0%, confirming the potential of this bioassay in the measurement of kanamycin in various applications. Our results also served as a good reference for developing similar fluorescent G4-DNA-based bioassays in the future.
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Affiliation(s)
- Yun-Peng Xing
- 1] State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 10084, China [2] School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050000, China
| | - Chun Liu
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050000, China
| | - Xiao-Hong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 10084, China
| | - Han-Chang Shi
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 10084, China
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19
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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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20
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LI X, TAN H, LI YL, WU ZY, SHEN GL, YU RQ. Aptamer-based Liquid Crystal Biosensor for Detection of Platelet-derived Growth Factor BB. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60729-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Schoukroun-Barnes LR, Wagan S, Wagan S, White RJ. Enhancing the analytical performance of electrochemical RNA aptamer-based sensors for sensitive detection of aminoglycoside antibiotics. Anal Chem 2014; 86:1131-7. [PMID: 24377296 DOI: 10.1021/ac4029054] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Folding-based electrochemical sensors utilizing structure-switching aptamers are specific, selective, sensitive, and widely applicable to the detection of a variety of target analytes. The specificity is achieved by the binding properties of an electrode-bound RNA or DNA aptamer biorecognition element. Signaling in this class of sensors arises from changes in electron transfer efficiency upon target-induced changes in the conformation/flexibility of the aptamer probe. These changes can be readily monitored electrochemically. Because of this signaling mechanism, there are several approaches to maximizing the analytical attributes (i.e., sensitivity, limit of detection, and observed binding affinity) of the aptamer sensor. Here, we present a systematic study of several approaches, including electrochemical interrogation parameters and biomolecular engineering of the aptamer sequence, to develop a sensor for the detection of aminoglycoside antibiotics. Specifically, through a combination of optimizing the electrochemical signal and engineering the parent 26-nucleotide RNA aptamer sequence to undergo larger conformation changes, we develop several improved sensors. These sensors exhibit binding affinities ranging from 220 nM to 42 μM, as much as a 100-fold improved limit of detection in comparison to previously reported sensors, and a variety of linear ranges including the therapeutic window for tobramycin. These data demonstrate that rational engineering of the aptamer structure to create large conformation changes upon target binding leads to improved sensor performance. We believe that the sensor design guidelines outlined here represent a general strategy for developing new aptamer folding-based electrochemical sensors.
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Affiliation(s)
- Lauren R Schoukroun-Barnes
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC) 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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22
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Luo Y, Zhang X, Yao D, Wen G, Liu Q, Liang A, Jiang Z. Resonance Rayleigh scattering detection of trace PDGF based on catalysis of an aptamer-modified nanogold probe in the Fehling reaction. RSC Adv 2014. [DOI: 10.1039/c4ra02857k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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23
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Liang J, Wei R, He S, Liu Y, Guo L, Li L. A highly sensitive and selective aptasensor based on graphene oxide fluorescence resonance energy transfer for the rapid determination of oncoprotein PDGF-BB. Analyst 2013; 138:1726-32. [PMID: 23359871 DOI: 10.1039/c2an36529d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oncoprotein platelet derived growth factor-BB (PDGF-BB) is one of the most critical growth factors that regulates tumor growth and division. In this work, a highly sensitive and selective fluorescence resonance energy transfer (FRET) aptasensor for PDGF-BB detection based on the assembly of dye-labeled aptamer and graphene oxide (GO) is developed for the first time. Due to the non-covalent assembly between aptamer and GO, fluorescence quenching of the dye takes place because of FRET. In the presence of PDGF-BB, the binding between aptamer and PDGF-BB will disturb the interaction between aptamer and GO, and release the dye-labeled aptamer from the GO surface, resulting in restoration of the fluorophore fluorescence. Because of the high fluorescence quenching efficiency, unique structure, and electronic properties of GO, the GO aptasensor exhibits extraordinarily high sensitivity. We also demonstrate that two highly related molecular variants of PDGF (AA, AB) can be distinguished from PDGF-BB, which indicates the aptasensor has excellent selectivity. Such an aptasensor opens a rapid, selective and sensitive route for the detection of PDGF-BB and provides a promising strategy for other cancer-related proteins detections.
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Affiliation(s)
- Junfei Liang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry & Environment, Beihang University, Beijing, 100191, PR China
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24
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Hu M, Zhang K. The application of aptamers in cancer research: an up-to-date review. Future Oncol 2013; 9:369-76. [PMID: 23469972 DOI: 10.2217/fon.12.201] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aptamers are nucleic acid ligands that are generated by molecular evolution to bind with high affinities and specificities to a large variety of targets, which make them attractive tools to be applied in cancer research. In this review, we highlight the recent progress in aptamer-based applications in cancer molecular research such as cancer targeting, biomarker discovery and therapeutics. Aptamers generated from cell-systematic evolution of ligands by exponential enrichment especially contribute to the discovery of novel membrane proteins as cancer biomarkers. Aptamer-nanoparticle conjugation could achieve higher affinity for cancer detection. Aptamer-conjugated nanocarriers deliver drugs to cancer cells with increased specificity and efficacy, as well as reduced toxicity.
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Affiliation(s)
- Meidi Hu
- Department of Gastroenterology, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, China
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25
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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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26
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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27
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Nucleic-Acid-binding chromophores as efficient indicators of aptamer-target interactions. J Nucleic Acids 2012; 2012:247280. [PMID: 23094140 PMCID: PMC3474971 DOI: 10.1155/2012/247280] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/01/2012] [Accepted: 09/03/2012] [Indexed: 12/02/2022] Open
Abstract
The binding affinity and specificity of nucleic acid aptamers have made them valuable candidates for use as sensors in diagnostic applications. In particular, chromophore-functionalized aptamers offer a relatively simple format for detection and quantification of target molecules. We describe the use of nucleic-acid-staining reagents as an effective tool for detecting and signaling aptamer-target interactions. Aptamers varying in size and structure and targeting a range of molecules have been used in conjunction with commercially available chromophores to indicate and quantify the presence of cognate targets with high sensitivity and selectivity. Our assay precludes the covalent modification of nucleic acids and relies on the differential fluorescence signal of chromophores when complexed with aptamers with or without their cognate target. We also evaluate factors that are critical for the stability of the complex between the aptamer and chromophore in presence or absence of target molecules. Our results indicate the possibility of controlling those factors to enhance the sensitivity of target detection by the aptamers used in such assays.
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28
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Aravind A, Yoshida Y, Maekawa T, Kumar DS. Aptamer-conjugated polymeric nanoparticles for targeted cancer therapy. Drug Deliv Transl Res 2012; 2:418-36. [DOI: 10.1007/s13346-012-0104-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Penmatsa V, Ruslinda AR, Beidaghi M, Kawarada H, Wang C. Platelet-derived growth factor oncoprotein detection using three-dimensional carbon microarrays. Biosens Bioelectron 2012; 39:118-23. [PMID: 22841446 DOI: 10.1016/j.bios.2012.06.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/13/2012] [Accepted: 06/29/2012] [Indexed: 01/31/2023]
Abstract
The potential of aptamers as ligand binding molecule has opened new avenues in the development of biosensors for cancer oncoproteins. In this paper, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor (PDGF-BB) oncoprotein detection is reported. The detection mechanism is based on the release of fluorophore (TOTO intercalating dye) from the target binding aptamer's stem structure when it captures PDGF. Amino-terminated three-dimensional carbon microarrays fabricated by pyrolyzing patterned photoresist were used as a detection platform. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5pmol. This detection strategy is promising in a wide range of applications in the detection of cancer biomarkers and other proteins.
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Affiliation(s)
- Varun Penmatsa
- Department of Mechanical and Materials Engineering, Florida International University, United States
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30
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Ruslinda AR, Penmatsa V, Ishii Y, Tajima S, Kawarada H. Highly sensitive detection of platelet-derived growth factor on a functionalized diamond surface using aptamer sandwich design. Analyst 2012; 137:1692-7. [PMID: 22349046 DOI: 10.1039/c2an15933c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamer-based fluorescence detection of platelet-derived growth factor (PDGF) on a functionalized diamond surface was demonstrated. In this work, a sandwich design based on the ability of PDGF to bind with aptamers at its two available binding sites was employed. It was found that this sandwich design approach significantly increases the fluorescence signal intensity, and thereby a very low detection limit of 4 pM was achieved. The effect of the ionic strength of MgCl(2) buffer solution was also investigated, and the most favourable binding for PDGF-BB occurred at a Mg(2+) concentration of 5.5 mM. Since the aptamers bind to the target PDGF with high affinity, fluorescence detection exhibited high selectivity towards different biomolecules. The high reproducibility of detection was confirmed by performing three cycles of measurements over a period of three days.
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Affiliation(s)
- A Rahim Ruslinda
- School of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan.
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31
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Leung CH, Chan DSH, He HZ, Cheng Z, Yang H, Ma DL. Luminescent detection of DNA-binding proteins. Nucleic Acids Res 2012; 40:941-55. [PMID: 21967849 PMCID: PMC3273792 DOI: 10.1093/nar/gkr763] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 01/07/2023] Open
Abstract
Transcription factors play a central role in cell development, differentiation and growth in biological systems due to their ability to regulate gene expression by binding to specific DNA sequences within the nucleus. The dysregulation of transcription factor signaling has been implicated in the pathogenesis of a number of cancers, developmental disorders, inflammation and autoimmunity. There is thus a high demand for convenient high-throughput methodologies able to detect sequence-specific DNA-binding proteins and monitor their DNA-binding activities. Traditional approaches for protein detection include gel mobility shift assays, DNA footprinting and enzyme-linked immunosorbent assays (ELISAs) which tend to be tedious, time-consuming, and may necessitate the use of radiographic labeling. By contrast, luminescence technologies offer the potential for rapid, sensitive and low-cost detection that are amenable to high-throughput and real-time analysis. The discoveries of molecular beacons and aptamers have spear-headed the development of new luminescent methodologies for the detection of proteins over the last decade. We survey here recent advances in the development of luminescent detection methods for DNA-binding proteins, including those based on molecular beacons, aptamer beacons, label-free techniques and exonuclease protection.
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Affiliation(s)
- Chung-Hang Leung
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Daniel Shiu-Hin Chan
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Hong-Zhang He
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Zhen Cheng
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Hui Yang
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
| | - Dik-Lung Ma
- Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao (China) and Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China)
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Xu W, Xiang Y, Ihms H, Lu Y. Label-Free Fluorescent Sensors Based on Functional Nucleic Acids. REVIEWS IN FLUORESCENCE 2010 2012. [DOI: 10.1007/978-1-4419-9828-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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33
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Cao ZJ, Peng QW, Qiu X, Liu CY, Lu JZ. Highly sensitive chemiluminescence technology for protein detection using aptamer-based rolling circle amplification platform. J Pharm Anal 2011; 1:159-165. [PMID: 29403694 PMCID: PMC5760798 DOI: 10.1016/j.jpha.2011.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 06/09/2011] [Indexed: 11/30/2022] Open
Abstract
A robust, selective and highly sensitive chemiluminescent (CL) platform for protein assay was presented in this paper. This novel CL approach utilized rolling circle amplification (RCA) as a signal enhancement technique and the 96-well plate as the immobilization and separation carrier. Typically, the antibody immobilized on the surface of 96-well plate was sandwiched with the protein target and the aptamer–primer sequence. This aptamer–primer sequence was then employed as the primer of RCA. Based on this design, a number of the biotinylated probes and streptavidin–horseradish peroxidase (SA–HRP) were captured on the plate, and the CL signal was amplified. In summary, our results demonstrated a robust biosensor with a detection limit of 10 fM that is easy to be established and utilized, and devoid of light source. Therefore, this new technique will broaden the perspective for future development of DNA-based biosensors for the detection of other protein biomarkers related to clinical diseases, by taking advantages of high sensitivity and selectivity.
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Affiliation(s)
- Zhi-Juan Cao
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qian-Wen Peng
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xue Qiu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Cai-Yun Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jian-Zhong Lu
- School of Pharmacy, Fudan University, Shanghai 201203, China
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34
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Chai Y, Tian D, Gu J, Cui H. A novel electrochemiluminescence aptasensor for protein based on a sensitive N-(aminobutyl)-N-ethylisoluminol-functionalized gold nanoprobe. Analyst 2011; 136:3244-51. [PMID: 21655607 DOI: 10.1039/c1an15298j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel electrochemiluminescence (ECL) aptasensor for platelet-derived growth factor B chain (PDGF-BB) assay was developed by assembling N-(aminobutyl)-N-ethylisoluminol functionalized gold nanoparticles (ABEI-AuNPs) with aptamers as nanoprobes. In the protocol, the biotinylated aptamer capture probes were first immobilized on a streptavidin coated gold nanoparticle (AuNPs) modified electrode, afterwards, the target PDGF-BB and the ABEI-AuNPs tagged aptamer signal probe were successively attached to the modified electrode by virtue of the dimer structure of PDGF-BB to fabricate a "sandwich" conjugate modified electrode, i.e. an aptasensor. ECL measurement was carried out with a double-step potential in carbonate buffer solution containing H(2)O(2). The aptasensor showed high sensitivity and selectivity toward PDGF-BB and specificity toward PDGF-BB aptamer. The detection limit was as low as 2.7 × 10(-14) M. In this work, the ABEI-AuNPs synthesized by a simple seed growth method have been successfully used as aptamer labels, which greatly amplified the ECL signal by binding numbers of ABEI molecules on the surface of AuNPs. The ABEI-AuNPs signal amplification is superior to other reported signal amplification strategies based on aptamer-related polymerase chain reaction or functionalized nanoparticles in simplicity, stability, labeling property and practical applicability. And the ABEI-AuNPs based nanoprobe is more sensitive than the luminol functionalized AuNPs based nanoprobe. Moreover, such an ultra-sensitive and low-cost assay can be accomplished with a simple and fast procedure by using a simple ECL instrumentation. The aptasensor was also applied for the detection of PDGF-BB in human serum samples, showing great application potential. Given these advantages, the ECL aptasensor is well suited for the direct, sensitive and rapid detection of protein in complex clinical samples.
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Affiliation(s)
- Ying Chai
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, People's Republic of China
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A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: application to label-free thrombin detection. Biosens Bioelectron 2011; 26:3346-52. [PMID: 21306887 DOI: 10.1016/j.bios.2011.01.015] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/09/2011] [Accepted: 01/13/2011] [Indexed: 11/20/2022]
Abstract
A new quantum dot (QD)-aptamer (apt) beacon that acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3(B), is demonstrated with label-free thrombin detection. The beacon, denoted as QD-apt:B, is constructed by (1) coupling of a single-stranded thrombin aptamer to Qdot 565 via EDC/Sulfo-NHS chemistry and (2) staining the duplex regions of the aptamer on QD with excess BOBO-3 before thrombin binding. When mixing a thrombin sample with QD-apt:B, BOBO-3 is competed away from the beacon due to target-induced aptamer folding, which then causes a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission and achieves thrombin quantitation. In this work, the effects of Mg(2+), coupling time, and aptamer type on the beacon's performances are investigated and discussed thoroughly with various methods, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and two-color differential gel electrophoresis. Using the best aptamer beacon (HTQ37), we attain highly specific and wide-range detection (from nM to μM) of thrombin in buffer, and the beacon can sense nM-range thrombin in 15% diluted serum. Compared to the reported QD aptamer assays, our method is advantageous from the aspect of using a simple sensory unit design without losing the detection sensitivity. Therefore, we consider the QD-apt:B beacon a potential alternative to immuno-reagents and an effective tool to study nucleic acid folding on QD as well.
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Functional Nucleic Acids for Fluorescence-Based Biosensing Applications. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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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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Li B, Dong S, Wang E. Homogeneous analysis: label-free and substrate-free aptasensors. Chem Asian J 2010; 5:1262-72. [PMID: 20408164 DOI: 10.1002/asia.200900660] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this Focus Review, we introduce a kind of "label-free" and "substrate-free" (LFSF) aptasensor that carries out the whole sensing process in a homogeneous solution. This means that commonly used covalent label; separation, and immobilization steps in biosensors are successfully avoided, which simplifies the sensing operations to the greatest degree. After brief description about the advantages of aptamers and "LFSF" aptasensors, the main content of the review is divided into fluorescent aptasenors, calorimetric aptasensors, and hemin-aptamer-DNAzyme "LFSF" aptasensors, which are three most widely developed sensing systems in this field. It is hoped that this review can provide an overall scene about how aptamers function as ideal recognition elements in smart analysis.
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Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022 P. R. China
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Li N. Detection of Non-Nucleic Acid Targets with an Unmodified Aptamer and a Fluorogenic Competitor. ACTA ACUST UNITED AC 2010; 15:189-197. [PMID: 20563298 DOI: 10.1016/j.jala.2010.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Aptamers are oligonucleotides that can bind to various non-nucleic acid targets, ranging from proteins to small molecules, with a specificity and affinity comparable to that of antibodies. Most aptamer-based detection strategies require modification on the aptamer, which could lead to a significant loss in its affinity and specificity to the target. Here we reported a generic strategy to design aptamer-based optical probes. An unmodified aptamer specific to the target and a fluorogenic competitor complementary to the aptamer are utilized for target recognition and signal generation, respectively. The competitor is a hairpin oligonucleotide with a fluorophore attached on one end and a quencher attached on the other. When no target is present, the competitor binds to the aptamer. However, when the target is introduced, the competitor will be displaced from the aptamer by the target, thus resulting in a target-specific decrease in fluorescence signal. Successful application of this strategy to different types of targets (small molecules and proteins) as well as different types of aptamers (DNA and RNA) has been demonstrated. Furthermore, a thermodynamics-based prediction model was established to further rationalize the optimization process. Due to its rapidness and simplicity, this aptamer-based detection strategy holds great promise in high throughput applications.
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Affiliation(s)
- Na Li
- University of Miami, Coral Gables, FL
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Csordas A, Gerdon A, Adams J, Qian J, Oh S, Xiao Y, Soh H. Detection of Proteins in Serum by Micromagnetic Aptamer PCR (MAP) Technology. Angew Chem Int Ed Engl 2010; 49:355-8. [DOI: 10.1002/anie.200904846] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andrew Csordas
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara (USA)
| | | | - Jonathan D. Adams
- Department of Physics, University of California, Santa Barbara (USA)
| | | | - Seung Soo Oh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - Yi Xiao
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - H. Tom Soh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
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Csordas A, Gerdon A, Adams J, Qian J, Oh S, Xiao Y, Soh H. Detection of Proteins in Serum by Micromagnetic Aptamer PCR (MAP) Technology. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Andrew Csordas
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara (USA)
| | | | - Jonathan D. Adams
- Department of Physics, University of California, Santa Barbara (USA)
| | | | - Seung Soo Oh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - Yi Xiao
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - H. Tom Soh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
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Zhang H, Li XF, Le XC. Differentiation and detection of PDGF isomers and their receptors by tunable aptamer capillary electrophoresis. Anal Chem 2009; 81:7795-800. [PMID: 19691297 DOI: 10.1021/ac901471w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tunable aptamer capillary electrophoresis (CE) techniques were developed to enable the separation and detection of platelet derived growth factor (PDGF) isomers and their receptors. Using an aptamer that formed a stable complex with the B chain but not with the A chain of PDGF, we were able to tweak the electrophoretic mobilities of the PDGF isomers for their separation. PDGF-AB bound to a single aptamer molecule was well resolved from PDGF-BB bound to two aptamer molecules. Simultaneous determination of 50 pM of two isomers was accomplished in a single analysis. Furthermore, PDGF-AB was used as a connector to bring receptor alpha and fluorescent aptamer into a single complex molecule. As a result, the formation of a (receptor alpha)-(PDGF-AB)-(fluorescent aptamer) ternary complex enabled the detection of the receptor alpha by tunable aptamer CE. A competitive assay was developed to determine receptor beta, making use of the competition between the receptor beta and fluorescent aptamer in binding to PDGF-BB. Detection limits were 0.5 nM for PDGF receptor alpha and 3 nM for receptor beta. Determination of PDGF isomers and their receptors in diluted serum samples showed no interference from the sample matrix.
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Affiliation(s)
- Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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Pu F, Huang Z, Hu D, Ren J, Wang S, Qu X. Sensitive, selective and label-free protein detection using a smart polymeric transducer and aptamer/ligand system. Chem Commun (Camb) 2009:7357-9. [PMID: 20024227 DOI: 10.1039/b918241a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have demonstrated a smart polymeric transducer and aptamer/intercalating dye system that allows the label-free detection of protein with high sensitivity and selectivity.
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Affiliation(s)
- Fang Pu
- State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
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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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Levy-Nissenbaum E, Radovic-Moreno AF, Wang AZ, Langer R, Farokhzad OC. Nanotechnology and aptamers: applications in drug delivery. Trends Biotechnol 2008; 26:442-9. [PMID: 18571753 DOI: 10.1016/j.tibtech.2008.04.006] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 04/03/2008] [Accepted: 04/18/2008] [Indexed: 12/17/2022]
Abstract
Nucleic acid ligands, also known as aptamers, are a class of macromolecules that are being used in several novel nanobiomedical applications. Aptamers are characterized by high affinity and specificity for their target, a versatile selection process, ease of chemical synthesis and a small physical size, which collectively make them attractive molecules for targeting diseases or as therapeutics. These properties will enable aptamers to facilitate innovative new nanotechnologies with applications in medicine. In this review, we will highlight recent developments in using aptamers in nanotechnology solutions for treating and diagnosing disease.
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Affiliation(s)
- Etgar Levy-Nissenbaum
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
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Degefa TH, Kwak J. Label-free aptasensor for platelet-derived growth factor (PDGF) protein. Anal Chim Acta 2008; 613:163-8. [PMID: 18395055 DOI: 10.1016/j.aca.2008.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 03/03/2008] [Accepted: 03/05/2008] [Indexed: 11/19/2022]
Abstract
A label-free aptasensor for platelet-derived growth factor (PDGF) protein is reported. The aptasensor uses mixed self-assembled monolayers (SAMs) composed of a thiol-modified PDGF binding aptamer and 6-mercaptohexanol (MCH) on a gold electrode. The SAMs were characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and differential pulse voltammetry (DPV) before and after binding of the protein using [Fe(CN)(6)](3-/4-), a redox marker ion as an indicator for the formation of a protein-aptamer complex. The CVs at the PDGF modified electrode showed significant differences, such as changes in the peak currents and peak-to-peak separation, before and after binding of the target protein. The EIS spectra, in the form of Nyquist plots, were analyzed with a Randles circuit while the electron transfer resistance R(ct) was used to monitor the binding of the target protein. The results showed that, without any modification to the aptamer, the target protein can be recognized effectively at the PDGF binding aptamer SAMs at the electrode surface. Control experiments using non-binding oligonucleotides assembled at the electrode surfaces also confirmed the results and showed that there was no formation of an aptamer-protein complex. The DPV signal at the aptamer functionalized electrode showed a linearly decreased marker ion peak current in a protein concentrations range of 1-40 nM. Thus, label-free detection of PDGF protein at an aptamer modified electrode has been demonstrated.
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Affiliation(s)
- Tesfaye Hailu Degefa
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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Alexis F, Rhee JW, Richie JP, Radovic-Moreno AF, Langer R, Farokhzad OC. New frontiers in nanotechnology for cancer treatment. Urol Oncol 2008; 26:74-85. [PMID: 18190835 DOI: 10.1016/j.urolonc.2007.03.017] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nanotechnology is a field of research at the crossroads of biology, chemistry, physics, engineering, and medicine. Design of multifunctional nanoparticles capable of targeting cancer cells, delivering and releasing drugs in a regulated manner, and detecting cancer cells with enormous specificity and sensitivity are just some examples of the potential application of nanotechnology to oncological diseases. In this review we discuss the recent advances of cancer nanotechnology with particular attention to nanoparticle systems that are in clinical practice or in various stages of development for cancer imaging and therapy.
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Affiliation(s)
- Frank Alexis
- Department of Anesthesiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Huang CC, Chiang CK, Lin ZH, Lee KH, Chang HT. Bioconjugated Gold Nanodots and Nanoparticles for Protein Assays Based on Photoluminescence Quenching. Anal Chem 2008; 80:1497-504. [DOI: 10.1021/ac701998f] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chih-Ching Huang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Cheng-Kang Chiang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Zong-Hong Lin
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Kun-Hong Lee
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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Pei R, Stojanovic MN. Study of thiazole orange in aptamer-based dye-displacement assays. Anal Bioanal Chem 2007; 390:1093-9. [PMID: 18165929 DOI: 10.1007/s00216-007-1773-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 11/16/2007] [Accepted: 11/20/2007] [Indexed: 11/24/2022]
Abstract
We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement approach is not always predictable, it is still a simple and sensitive assay to detect binding between RNA aptamers and small molecules. In particular, we describe efficient assays for tobramycin and theophylline, with up to 90% displacement of TO observed, and we describe the first aptameric assay for cAMP.
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Affiliation(s)
- Renjun Pei
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA.
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Abstract
Botulinum neurotoxin (BoNT), which cause the deadly neuroparalytic disease, botulism, is the most toxic substance known to man. BoNT can be used as potential bioterrorism agents, and therefore, pose great threat to national security and public health. Rapid and sensitive detection of BoNTs using molecular and biochemical techniques is an essential component in the diagnosis of botulism, and is yet to be achieved. The most sensitive and widely accepted assay method for BoNTs is mouse bioassay, which takes 4 days to complete. This clearly can not meet the need for clinical diagnosis of botulism, botulinum detection in field conditions, and screening of large scale samples. Consequently, the clinical diagnosis of botulism relies on the clinical symptom development, thus limiting the effectiveness of antitoxin treatment. In response to this critical need, many in vitro methods for BoNT detection are under development. This review is focused on recently developed in vitro detection methods for BoNTs, and emerging new technologies with potential for sensitive and rapid in vitro diagnostics for botulism.
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Affiliation(s)
- Shuowei Cai
- Botulinum Research Center, and Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, USA.
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