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Zhu F, Zhao Q. CRISPR/Cas12a linked sandwich aptamer assay for sensitive detection of thrombin. Anal Chim Acta 2024; 1287:342106. [PMID: 38182384 DOI: 10.1016/j.aca.2023.342106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Thrombin is a serine protease and hemostasis regulator with multiple functions and recognized as an important biomarker for diseases, and sensitive detection of thrombin is of significance for clinical diagnostics and disease monitoring. Recently, the target-triggered nonspecific single-stranded deoxyribonuclease activity of CRISPR/Cas system is discovered, making it become a powerful tool in assay developments due to the ease of signal amplification. In the short period of development, many CRISPR based nucleic acid detection methods have already played a critical role in clinical diagnostics. However, the application of CRISPR/Cas system for protein biomarkers remains limited. RESULTS Here we describe a CRISPR/Cas12a linked sandwich aptamer assay for detection of thrombin, which was based on the formation of a sandwich complex of target by using a capture aptamer or antibody coated on the microplate and a well-designed detection DNA strand. The detection DNA strand contained an anti-thrombin aptamer and an active DNA of Cas12a, thus the sandwich complex was labeled with the active DNA. The active DNA triggered activity of Cas12a in indiscriminately cleaving fluorophore and quencher labeled DNA reporters, causing significant fluorescence increase. Our method enabled sensitive detection of thrombin down to 10 pM, and it showed high selectivity for thrombin. The assay exhibited good performance in diluted serum samples, demonstrating the applicability for thrombin analysis in the real media. SIGNIFICANCE This assay combines the merits of high affinity of aptamer, trans-cleavage activity of Cas12a, high selectivity of sandwich format analysis, and high-throughput detection of microplate assay, and it shows promise in applications.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China.
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2
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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3
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Xiao X, Zhen S. Recent advances in fluorescence anisotropy/polarization signal amplification. RSC Adv 2022; 12:6364-6376. [PMID: 35424604 PMCID: PMC8982260 DOI: 10.1039/d2ra00058j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 12/25/2022] Open
Abstract
Fluorescence anisotropy/polarization is an attractive and versatile technique based on molecular rotation in biochemical/biophysical systems. Traditional fluorescence anisotropy/polarization assays showed relatively low sensitivity for molecule detection, because widespread molecular masses are too small to produce detectable changes in fluorescence anisotropy/polarization value. In this review, we discuss in detail how the potential of fluorescence anisotropy/polarization signal approach considerably expanded through the implementation of mass amplification, recycle the target amplification, fluorescence probes structure-switching amplification, resonance energy transfer amplification, and provide perspectives at future directions and applications.
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Affiliation(s)
- Xue Xiao
- Key Laboratory of Basic Chemistry of the State Ethnic Commission, College of Chemistry and Environment, Southwest Minzu University 610041 Chengdu PR China
| | - Shujun Zhen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University 400715 Chongqing PR China
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4
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Weaver SD, Whelan RJ. Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1302-1307. [PMID: 33533761 DOI: 10.1039/d0ay02256j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aptamers have many useful attributes including specific binding to molecular targets. After aptamers are identified, their target binding must be characterized. Fluorescence anisotropy (FA) is one technique that can be used to characterize affinity and to optimize aptamer-target interactions. Efforts to make FA assays more efficient by reducing assay volume and time from mixing to measurement may save time and resources by minimizing consumption of costly reagents. Here, we use thrombin and two thrombin-binding aptamers as a model system to show that plate-based FA experiments can be performed in volumes as low as 2 μL per well with 20 minute incubations with minimal loss in assay precision. We demonstrate that the aptamer-thrombin interaction is best modelled with the Hill equation, indicating cooperative binding. The miniaturization of this assay has implications in drug development, as well as in the efficiency of aptamer selection workflows by allowing for higher throughput aptamer analysis.
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Affiliation(s)
- Simon D Weaver
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca J Whelan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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5
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Bai Y, Shu T, Su L, Zhang X. Functional nucleic acid-based fluorescence polarization/anisotropy biosensors for detection of biomarkers. Anal Bioanal Chem 2020; 412:6655-6665. [PMID: 32601896 DOI: 10.1007/s00216-020-02754-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023]
Abstract
The sensitive and selective detection of biomarkers plays a crucial role in disease diagnostics, drug discovery, and early screening of cancers. The achievement of this goal highly depends on the continuous development of biosensing technologies. Among them, fluorescence anisotropy/polarization (FA/FP) analysis receives increasing interest due to the advantage of simple operation, fast response, and no background interference. In recent decades, great progress has been achieved in FA/FP sensors thanks to the development of functional nucleic acids (FNAs) including aptamers and nucleic acid enzymes. This review focuses on FNA-based FA/FP sensors for the quantitative detection of biomarkers, such as nucleic acid, small molecules, and proteins. The design strategies, recognition elements, and practical applications are fully highlighted. The article also discusses the challenges of applying FNA-based FA/FP sensors in the next generation and the potential solutions along with future prospects. Graphical abstract.
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Affiliation(s)
- Yunlong Bai
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tong Shu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China. .,Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, Guangdong, China.
| | - Lei Su
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China. .,School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, Guangdong, China.
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6
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Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review. Anal Chim Acta 2020; 1125:267-278. [PMID: 32674773 DOI: 10.1016/j.aca.2020.05.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 12/26/2022]
Abstract
Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.
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7
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Zhao Q, Bai Y, Wang H. Directing a rational design of aptamer-based fluorescence anisotropy assay for sensitive detection of immunoglobulin E by site-specific binding study. Talanta 2020; 217:121018. [PMID: 32498825 DOI: 10.1016/j.talanta.2020.121018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 11/17/2022]
Abstract
Mapping aptamer-protein interactions is important for characterization and applications of aptamers against proteins. We describe here probing affinity interactions between aptamer and immunoglobulin E (IgE) with a fluorescence anisotropy (FA) approach using a series of aptamer probes having single fluorescein (FAM) label at individual nucleotide (A, C, T). Studies of binding between IgE and aptamer probes revealed several possible close-contact sites, e.g., T9, T10, T11, T13, C15, and T17 of a 37-nt aptamer with a stem-loop secondary structure. FAM labeling on these sites resulted in much higher FA values (higher than 0.230 for T10, T11, T13 and C15) of aptamer-IgE complexes than the distant sites (e.g., terminals) of aptamer probably because the bound IgE close to these sites significantly restricted local rotation of FAM. Close-contact site labeled aptamer probes with high affinity allowed to develop a more sensitive FA assay for IgE than distant site labeled aptamers. The FA assay using T10-labeled aptamer with a dissociation constant (Kd) about 0.8 nM enabled selective detection of IgE at 20 pM and large FA increase upon IgE addition. We also found A12, C14, A25, and T27 were important for IgE-aptamer binding as FAM labeling at these sites significantly reduced aptamer affinity. FA study showed the loop region of this stem-loop aptamer was crucial for affinity binding, and IgE bound to the loop. This FA method will be helpful for understanding aptamer-protein binding and making a rational design of aptamer affinity assays for proteins.
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Affiliation(s)
- Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yunlong Bai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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8
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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9
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Minagawa H, Shimizu A, Kataoka Y, Kuwahara M, Kato S, Horii K, Shiratori I, Waga I. Fluorescence Polarization-Based Rapid Detection System for Salivary Biomarkers Using Modified DNA Aptamers Containing Base-Appended Bases. Anal Chem 2020; 92:1780-1787. [PMID: 31855403 DOI: 10.1021/acs.analchem.9b03450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The field of care testing toward the analysis of blood and saliva lacks nowadays simple test techniques for biomarkers. In this study, we have developed a novel nucleobase analog, Ugu, which is a uracil derivative bearing a guanine base at the 5-position. Moreover, we attempted the development of aptamers that can bind to secretory immunoglobulin A (SIgA), which has been examined as a stress marker in human saliva. It was observed that the acquired aptamer binds strongly and selectively to the SIgA dimer (Kd = 13.6 nM) without binding to the IgG and IgA monomers of human serum. Reduction of the aptamer length (41 mer) successfully improved 4-fold the binding affinity (Kd = 3.7 nM), compared to the original, longer aptamer (78 mer). Furthermore, the development of a simple detection system for human saliva samples by fluorescence polarization was investigated, using the reported human salivary α-amylase (sAA) and the SIgA-binding aptamer. Comparison of the present method with conventional enzyme-linked immunosorbent assay techniques highlighted a significant Pearson's correlation of 0.94 and 0.83 when targeting sAA and SIgA, respectively. It is thus strongly suggested that a new simple test of stress markers in human saliva can be quantified quickly without bound/free (B/F) separation.
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Affiliation(s)
- Hirotaka Minagawa
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Akihisa Shimizu
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Yuka Kataoka
- Graduate School of Integrated Basic Sciences , Nihon University , 3-25-40 Sakurajosui, Setagaya-ku , Tokyo 156-8550 , Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences , Nihon University , 3-25-40 Sakurajosui, Setagaya-ku , Tokyo 156-8550 , Japan
| | - Shintaro Kato
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Katsunori Horii
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Ikuo Shiratori
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Iwao Waga
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
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10
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Lee K, Lee J, Ahn B. Design of Refolding DNA Aptamer on Single-Walled Carbon Nanotubes for Enhanced Optical Detection of Target Proteins. Anal Chem 2019; 91:12704-12712. [DOI: 10.1021/acs.analchem.9b02177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | - Jeeyeon Lee
- Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
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11
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Lan Y, Qin G, Wei Y, Dong C, Wang L. Highly sensitive analysis of tetrodotoxin based on free-label fluorescence aptamer sensing system. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:411-418. [PMID: 31059893 DOI: 10.1016/j.saa.2019.04.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
Tetrodotoxin (TTX) specifically can bind to its nucleic acid aptamer (TTX-aptamer) and cause the conformation of TTX-aptamer to be switched from the single-strand random coiling form to the compact neck ring structure. Based on the microenvironment difference of the fluorescence reporter, berberine in between the single-stranded coil oligonucleotides and the structure of the neck ring, a simple, rapid and sensitive label-free fluorescence aptamer sensing system for detection of TTX was developed. Various factors affecting the analysis of TTX were optimized, including the concentration of berberine, ion strength, pH, reaction time, the concentration of TTX-aptamer. Under the optimal experimental conditions, the fluorescence intensity of the sensing system and the concentration of TTX showed a good linear relationship in the range of 0.1 nM to 500 nM, with the detection limit of 0.074 nM. The standard recovery test result exhibited that the recoveries of TTX in serum samples were 96.54%-106.40%. The established method has the advantages of high specificity, good sensitivity, quickness and convenience, low cost, and can be used for the detection of TTX in serum samples.
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Affiliation(s)
- Yifeng Lan
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, PR China
| | - Guojie Qin
- Institute of Horticulture, Shanxi Academy of Agriculture Science, Taiyuan 030031, PR China
| | - Yanli Wei
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, PR China.
| | - Chuan Dong
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, PR China
| | - Li Wang
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, PR China
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12
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Gan H, Wu J, Ju H. Proximity hybridization-induced on particle DNA walker for ultrasensitive protein detection. Anal Chim Acta 2019; 1074:142-149. [PMID: 31159934 DOI: 10.1016/j.aca.2019.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 05/05/2019] [Indexed: 11/15/2022]
Abstract
A simple proximity hybridization-induced on particle DNA walker was designed for ultrasensitive detection of proteins, for example platelet-derived growth factor (PDGF-BB) secreted by cancer cells, in which the DNA walker was activated by specific target binding and powered by an enzymatic cleavage to produce amplified signal. High-density FAM-labeled hairpin oligonucleotides (FAM-DNA1) were functionalized on AuNPs to construct three-dimensional (3D) DNA tracks. The specific binding of PDGF-BB with two aptamer probes (DNA3 and DNA4) led to the proximity hybridization-induced DNA displacement and the free of DNA walker (DNA2) to perform movement on the 3D tracks by an enzymatic cleavage, resulting in the release of massive FAM-DNA1 fragments from the AuNPs and the generation of fluorescent signal. This DNA walker based sensing strategy could detect PDGF-BB in a concentration range of 4 orders of magnitude with a detection limit down to sub-pM level. The practical applicability of the assay was demonstrated by detecting PDGF-BB secreted from MCF-7 cells with satisfactory results. The proposed DNA walker based assay could conveniently detect PDGF-BB with high sensitivity and good accuracy, along with the good extensibility of the assay, showing promise for practical diagnosis.
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Affiliation(s)
- Haiying Gan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Jie Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
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13
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Transition metal complexes based aptamers as optical diagnostic tools for disease proteins and biomolecules. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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14
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Lisi S, Fiore E, Scarano S, Pascale E, Boehman Y, Ducongé F, Chierici S, Minunni M, Peyrin E, Ravelet C. Non-SELEX isolation of DNA aptamers for the homogeneous-phase fluorescence anisotropy sensing of tau Proteins. Anal Chim Acta 2018; 1038:173-181. [DOI: 10.1016/j.aca.2018.07.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 02/07/2023]
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15
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Morris FD, Peterson EM, Heemstra JM, Harris JM. Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer Assembly. Anal Chem 2018; 90:12964-12970. [PMID: 30280568 DOI: 10.1021/acs.analchem.8b03637] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aptamers are short nucleic-acid biopolymers selected to have high affinity and specificity for protein or small-molecule target analytes. Aptamers can be engineered into split-aptamer biosensors comprising two nucleic acid strands that coassemble as they bind to a target, resulting in a large signal change from attached molecular probes (e.g., molecular beacons). The kinetics of split-aptamer assembly and their dependence on target recognition are largely unknown; knowledge of these kinetics could help in design and optimization of split-aptamer biosensors. In this work, we measure assembly kinetics of cocaine-dependent split-aptamer molecules using single-molecule fluorescence imaging. Assembly is monitored between a DNA strand tethered to a glass substrate and solutions containing the other strand tagged with a fluorescent label, with varying concentrations of the cocaine analyte. Dissociation rates are measured by tracking individual molecules and measuring their bound lifetimes. Dissociation-time distributions are biexponential, possibly indicating different folded states of the aptamer. The dissociation rate of only the longer-lived complex decreases with cocaine concentration, suggesting that cocaine stabilizes the long-lived aptamer complex. The variation in the slow dissociation rate with cocaine concentration is well described with an equilibrium-binding model, where the dissociation rate approaches a saturation limit consistent with the dissociation-equilibrium constant for cocaine-binding to the split aptamer. This single-molecule methodology provides a sensitive readout of cocaine-binding based on the dissociation kinetics of the split aptamer, allowing one to distinguish target-dependent aptamer assembly from background assembly. This methodology could be used to study other systems where target association affects the stability of aptamer duplexes.
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Affiliation(s)
- Frances D Morris
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Eric M Peterson
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Jennifer M Heemstra
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , United States
| | - Joel M Harris
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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16
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Nasiri Khonsari Y, Sun S. Recent trends in electrochemiluminescence aptasensors and their applications. Chem Commun (Camb) 2018; 53:9042-9054. [PMID: 28759057 DOI: 10.1039/c7cc04300g] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aptamers are single stranded DNA or RNA ligands which can be selected for different targets from proteins to small organic dyes. In the past few years great progress has been accomplished in the development of aptamer based bioanalytical assays with different detection techniques. Among them, electrochemiluminescence (ECL) aptasensors are very promising because they have the advantages of both electrochemical and chemiluminescence biosensors, such as high sensitivity, low background, cost effectiveness, and ease of control. In this review, we summarize the recent efforts to construct novel and improved ECL aptasensors and their application.
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Affiliation(s)
- Yasamin Nasiri Khonsari
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi, District, Dalian 116023, China
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17
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Samokhvalov AV, Safenkova IV, Eremin SA, Zherdev AV, Dzantiev BB. Measurement of (Aptamer–Small Target) KD Using the Competition between Fluorescently Labeled and Unlabeled Targets and the Detection of Fluorescence Anisotropy. Anal Chem 2018; 90:9189-9198. [DOI: 10.1021/acs.analchem.8b01699] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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18
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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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19
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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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20
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Morii T. A Bioorganic Chemistry Approach to Understanding Molecular Recognition in Protein–Nucleic Acid Complexes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011
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21
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Meirinho SG, Dias LG, Peres AM, Rodrigues LR. Electrochemical aptasensor for human osteopontin detection using a DNA aptamer selected by SELEX. Anal Chim Acta 2017; 987:25-37. [PMID: 28916037 DOI: 10.1016/j.aca.2017.07.071] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/30/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
Abstract
A DNA aptamer with affinity and specificity for human osteopontin (OPN), a potential breast cancer biomarker, was selected using the SELEX process, considering its homology rate and the stability of its secondary structures. This aptamer exhibited a satisfactory affinity towards OPN, showing dissociation constants lower than 2.5 nM. It was further used to develop a simple, label-free electrochemical aptasensor against OPN. The aptasensor showed good sensitivity towards OPN in standard solutions, being the square wave voltammetry (SWV), compared to the cyclic voltammetry, the most sensitive technique with detection and quantification limits of 1.4 ± 0.4 nM and 4.2 ± 1.1 nM, respectively. It showed good reproducibility and acceptable selectivity, exhibiting low signal interferences from other proteins, as thrombin, with 2.6-10 times lower current signals-off than for OPN. The aptasensor also successfully detected OPN in spiked synthetic human plasma. Using SWV, detection and quantification limits (1.3 ± 0.1 and 3.9 ± 0.4 nM) within the OPN plasma levels reported for patients with breast cancer (0.4-4.5 nM) or with metastatic or recurrent breast cancer (0.9-8.4 nM) were found. Moreover, preliminary assays, using a sample of human plasma, showed that the aptasensor and the standard ELISA method quantified similar OPN levels (2.2 ± 0.7 and 1.7 ± 0.1 nM, respectively). Thus, our aptasensor coupled with SWV represents a promising alternative for the detection of relevant breast cancer biomarkers.
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Affiliation(s)
- Sofia G Meirinho
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luís G Dias
- ESA - Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CQ-VR - Centro de Química - Vila Real, University of Trás-os-Montes, Apartado 1013, 5001-801 Vila Real, Portugal
| | - António M Peres
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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22
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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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23
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Lu L, Mao Z, Kang TS, Leung CH, Ma DL. A versatile nanomachine for the sensitive detection of platelet-derived growth factor-BB utilizing a G-quadruplex-selective iridium(III) complex. Biosens Bioelectron 2016; 85:300-309. [DOI: 10.1016/j.bios.2016.05.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/13/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
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24
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Guo L, Zhao Q. Determination of the platelet-derived growth factor BB by a competitive thrombin-linked aptamer-based Fluorometric assay. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1978-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Ma DL, Wang M, Liu C, Miao X, Kang TS, Leung CH. Metal complexes for the detection of disease-related protein biomarkers. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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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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27
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Qin C, Wen W, Zhang X, Gu H, Wang S. Visual detection of thrombin using a strip biosensor through aptamer-cleavage reaction with enzyme catalytic amplification. Analyst 2016; 140:7710-7. [PMID: 26451394 DOI: 10.1039/c5an01712b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new class of strip biosensors has been established based on well-distributed thrombin aptamer-linked gold nanoparticle aggregates, which will undergo a cracking reaction when the target recognizes its homologous aptamer. Combining the aptamer-cleavage reaction with the enzyme catalytic amplification system, our proposed lateral flow strip biosensor (LFB) is capable of visually detecting 6.4 pM of thrombin without instrumentation within 12 minutes. Under the optimal conditions, the quantitative detection of thrombin by a portable strip reader exhibited a linear relationship between the peak area and the concentration of thrombin in the range of 6.4 pM-500 nM with a detection limit of 4.9 pM, which is three orders of magnitude lower than that of the aptamer-functionalized gold nanoparticle-based LFB (2.5 nM, Xu et al., Anal. Chem., 2009, 81, 669-675). As the aptamers have no special requirements and the gold nanoparticles can also be replaced by other metallic nanoparticles, this method for strip sensing is expected to be generally applicable in point of care testing, home testing, medical diagnostics, clinical diagnosis, and environmental monitoring.
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Affiliation(s)
- Chunyan Qin
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Wei Wen
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Haoshuang Gu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
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28
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Thrombin-linked aptamer assay for detection of platelet derived growth factor BB on magnetic beads in a sandwich format. Talanta 2016; 158:159-164. [PMID: 27343590 DOI: 10.1016/j.talanta.2016.05.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/10/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022]
Abstract
Here we describe a thrombin-linked aptamer assay (TLAA) for protein by using thrombin as an enzyme label, harnessing enzyme activity of thrombin and aptamer affinity binding. TLAA converts detection of specific target proteins to the detection of thrombin by using a DNA sequence that consists of two aptamers with the first aptamer binding to the specific target protein and the second aptamer binding to thrombin. Through the affinity binding, the thrombin enzyme is labeled on the protein target, and thrombin catalyzes the hydrolysis of small peptide substrate into product, generating signals for quantification. As a proof of principle, we show a sandwich TLAA for platelet derived growth factor BB (PDGF-BB) by using anti-PDGF-BB antibody coated on magnetic beads and an oligonucleotide containing the aptamer for PDGF-BB and the aptamer for thrombin. The binding of PDGF-BB to both the antibody and the aptamer results in labeling the complex with thrombin. We achieved detection of PDGF-BB at 16 pM. This TLAA contributes a new application of thrombin and its aptamer in bioanalysis, and shows potentials in assay developments.
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29
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Interaction between gluten proteins and their mixtures with water-extractable arabinoxylan of wheat by rheological, molecular anisotropy and CP/MAS 13C NMR measurements. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-015-2622-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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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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31
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Hu P, Yang B. Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay. Talanta 2015; 147:276-81. [PMID: 26592607 DOI: 10.1016/j.talanta.2015.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/27/2022]
Abstract
Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays.
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Affiliation(s)
- Pan Hu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, PR China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, PR China.
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32
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Zhao J, Ma Y, Kong R, Zhang L, Yang W, Zhao S. Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity. Anal Chim Acta 2015; 887:216-223. [DOI: 10.1016/j.aca.2015.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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33
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Huang Y, Liu X, Huang H, Qin J, Zhang L, Zhao S, Chen ZF, Liang H. Attomolar detection of proteins via cascade strand-displacement amplification and polystyrene nanoparticle enhancement in fluorescence polarization aptasensors. Anal Chem 2015; 87:8107-14. [PMID: 26169378 DOI: 10.1021/ac5041692] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Extremely sensitive and accurate measurements of protein markers for early detection and monitoring of diseases pose a formidable challenge. Herein, we develop a new type of amplified fluorescence polarization (FP) aptasensor based on allostery-triggered cascade strand-displacement amplification (CSDA) and polystyrene nanoparticle (PS NP) enhancement for ultrasensitive detection of proteins. The assay system consists of a fluorescent dye-labeled aptamer hairpin probe and a PS NP-modified DNA duplex (assistant DNA/trigger DNA duplex) probe with a single-stranded part and DNA polymerase. Two probes coexist stably in the absence of target, and the dye exhibits relatively low FP background. Upon recognition and binding with a target protein, the stem of the aptamer hairpin probe is opened, after which the opened hairpin probe hybridizes with the single-stranded part in the PS NP-modified DNA duplex probe and triggers the CSDA reaction through the polymerase-catalyzed recycling of both target protein and trigger DNA. Throughout this CSDA process, numerous massive dyes are assembled onto PS NPs, which results in a substantial FP increase that provides a readout signal for the amplified sensing process. Our newly proposed amplified FP aptasensor enables the quantitative measurement of proteins with the detection limit in attomolar range, which is about 6 orders of magnitude lower than that of traditional homogeneous aptasensors. Moreover, this sensing method also exhibits high specificity for target proteins and can be performed in homogeneous solutions. In addition, the suitability of this method for the quantification of target protein in biological samples has also been shown. Considering these distinct advantages, the proposed sensing method can be expected to provide an ultrasensitive platform for the analysis of various types of target molecules.
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Affiliation(s)
- Yong Huang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Xiaoqian Liu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Huakui Huang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Jian Qin
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Liangliang Zhang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Zhen-Feng Chen
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
| | - Hong Liang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, China
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Yin J, Zhang A, Dong C, Ren J. An aptamer-based single particle method for sensitive detection of thrombin using fluorescent quantum dots as labeling probes. Talanta 2015; 144:13-9. [PMID: 26452786 DOI: 10.1016/j.talanta.2015.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 01/28/2023]
Abstract
In this study, an aptamer-based single particle method was developed for the thrombin detection in human serum samples using fluorescence correlation spectroscopy (FCS). In this method, quantum dots (QDs) were used as the fluorescent probes and thrombin-binding aptamer (TBA) was used as molecular recognition unit. When two QDs probes labeled with TBA (QD-TBA1 and QD-TBA2) are mixed in a sample containing thrombin targets, the binding of targets will cause QDs to form dimers (or oligomers) with bigger sizes, which leads to the nearly double increase in the characteristic diffusion time of QDs in the detection volume of FCS. FCS method can detect the change in the characteristic diffusion time of QDs. Firstly, the diffusion and blinking behaviors of QD-TBA probes in the presence of thrombin were investigated by FCS and total internal reflection fluorescence microscopy (TIRFM) imaging system, and the experimental results documented that QD-TBAs were bound together with "one-by-one" structure when thrombin were added into the solution. And then, the assay conditions were optimized in order to improve the sensitivity and specificity of this method. Under the optimized conditions, the linear range of the method is from 5.0 nM to 500 nM of thrombin, and the limit of detection is about 2.6 nM. Finally, this method was applied to homogeneous determination of thrombin in human serum samples.
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Affiliation(s)
- Jinjin Yin
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Aidi Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
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35
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Peeters M, van Grinsven B, Cleij TJ, Jiménez-Monroy KL, Cornelis P, Pérez-Ruiz E, Wackers G, Thoelen R, De Ceuninck W, Lammertyn J, Wagner P. Label-free Protein Detection Based on the Heat-Transfer Method--A Case Study with the Peanut Allergen Ara h 1 and Aptamer-Based Synthetic Receptors. ACS APPLIED MATERIALS & INTERFACES 2015; 7:10316-10323. [PMID: 25916249 DOI: 10.1021/acsami.5b00994] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aptamers are an emerging class of molecules that, because of the development of the systematic evolution of ligands by exponential enrichment (SELEX) process, can recognize virtually every target ranging from ions, to proteins, and even whole cells. Although there are many techniques capable of detecting template molecules with aptamer-based systems with high specificity and selectivity, they lack the possibility of integrating them into a compact and portable biosensor setup. Therefore, we will present the heat-transfer method (HTM) as an interesting alternative because this offers detection in a fast and low-cost manner and has the possibility of performing experiments with a fully integrated device. This concept has been demonstrated for a variety of applications including DNA mutation analysis and screening of cancer cells. To the best our knowledge, this is the first report on HTM-based detection of proteins, in this case specifically with aptamer-type receptors. For proof-of-principle purposes, measurements will be performed with the peanut allergen Ara h 1 and results indicate detection limits in the lower nanomolar regime in buffer liquid. As a first proof-of-application, spiked Ara h 1 solutions will be studied in a food matrix of dissolved peanut butter. Reference experiments with the quartz-crystal microbalance will allow for an estimate of the areal density of aptamer molecules on the sensor-chip surface.
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Affiliation(s)
- Marloes Peeters
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ‡School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Bart van Grinsven
- §Maastricht Science Programme, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Thomas J Cleij
- §Maastricht Science Programme, Maastricht University, 6200 MD Maastricht, The Netherlands
| | | | - Peter Cornelis
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- #BIOSYST-MeBioS, KU Leuven-University of Leuven, Willem de Crooylan 42, 3000 Leuven, Belgium
| | - Gideon Wackers
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
| | - Ronald Thoelen
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ⊥Division IMOMEC, IMEC v.z.w. , Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Ward De Ceuninck
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ⊥Division IMOMEC, IMEC v.z.w. , Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Jeroen Lammertyn
- #BIOSYST-MeBioS, KU Leuven-University of Leuven, Willem de Crooylan 42, 3000 Leuven, Belgium
| | - Patrick Wagner
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
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Kang L, Yang B, Zhang X, Cui L, Meng H, Mei L, Wu C, Ren S, Tan W. Enzymatic cleavage and mass amplification strategy for small molecule detection using aptamer-based fluorescence polarization biosensor. Anal Chim Acta 2015; 879:91-6. [PMID: 26002482 DOI: 10.1016/j.aca.2015.03.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/18/2015] [Accepted: 03/21/2015] [Indexed: 11/25/2022]
Abstract
Fluorescence polarization (FP) assays incorporated with fluorophore-labeled aptamers have attracted great interest in recent years. However, detecting small molecules through the use of FP assays still remains a challenge because small-molecule binding only results in negligible changes in the molecular weight of the fluorophore-labeled aptamer. To address this issue, we herein report a fluorescence polarization (FP) aptamer assay that incorporates a novel signal amplification strategy for highly sensitive detection of small molecules. In the absence of adenosine, our model target, free FAM-labeled aptamer can be digested by nuclease, resulting in the release of FAM-labeled nucleotide segments from the dT-biotin/streptavidin complex with weak background signal. However, in the presence of target, the FAM-labeled aptamer-target complex protects the FAM-labeled aptamer from nuclease cleavage, allowing streptavidin to act as a molar mass amplifier. The resulting increase in molecular mass and FP intensity of the aptamer-target complex provides improved sensitivity for concentration measurement. The probe could detect adenosine from 0.5 μM to 1000 μM, with a detection limit of 500 nM, showing that the sensitivity of the probe is superior to aptamer-based FP approaches previously reported for adenosine. Importantly, FP could resist environmental interferences, making it useful for complex biological samples without any tedious sample pretreatments. Our results demonstrate that this dual-amplified, aptamer-based strategy can be used to design fluorescence polarization probes for rapid, sensitive, and selective measurement of small molecules in complicated biological environment.
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Affiliation(s)
- Liping Kang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Bin Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China.
| | - Liang Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Hongmin Meng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Lei Mei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Cuichen Wu
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
| | - Songlei Ren
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, Hunan 410082, China; Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
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Li N, Su X, Lu Y. Nanomaterial-based biosensors using dual transducing elements for solution phase detection. Analyst 2015; 140:2916-43. [PMID: 25763412 DOI: 10.1039/c4an02376e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Biosensors incorporating nanomaterials have demonstrated superior performance compared to their conventional counterparts. Most reported sensors use nanomaterials as a single transducer of signals, while biosensor designs using dual transducing elements have emerged as new approaches to further improve overall sensing performance. This review focuses on recent developments in nanomaterial-based biosensors using dual transducing elements for solution phase detection. The review begins with a brief introduction of the commonly used nanomaterial transducers suitable for designing dual element sensors, including quantum dots, metal nanoparticles, upconversion nanoparticles, graphene, graphene oxide, carbon nanotubes, and carbon nanodots. This is followed by the presentation of the four basic design principles, namely Förster Resonance Energy Transfer (FRET), Amplified Fluorescence Polarization (AFP), Bio-barcode Assay (BCA) and Chemiluminescence (CL), involving either two kinds of nanomaterials, or one nanomaterial and an organic luminescent agent (e.g. organic dyes, luminescent polymers) as dual transducers. Biomolecular and chemical analytes or biological interactions are detected by their control of the assembly and disassembly of the two transducing elements that change the distance between them, the size of the fluorophore-containing composite, or the catalytic properties of the nanomaterial transducers, among other property changes. Comparative discussions on their respective design rules and overall performances are presented afterwards. Compared with the single transducer biosensor design, such a dual-transducer configuration exhibits much enhanced flexibility and design versatility, allowing biosensors to be more specifically devised for various purposes. The review ends by highlighting some of the further development opportunities in this field.
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Affiliation(s)
- Ning Li
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, 117602 Singapore.
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Huang H, Wei H, Zou M, Xu X, Xia B, Liu F, Li N. Modulating fluorescence anisotropy of terminally labeled double-stranded DNA via the interaction between dye and nucleotides for rational design of DNA recognition based applications. Anal Chem 2015; 87:2748-54. [PMID: 25671552 DOI: 10.1021/ac504028n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Effective signal enhancement for fluorescence anisotropy in a simple manner is most desirable for fluorescence anisotropy method development. This work aimed to provide insights into the fluorescence anisotropy of terminally labeled double-stranded DNA (dsDNA) to facilitate a facile and universal design strategy for DNA recognition based applications. We demonstrated that fluorescence anisotropy of dsDNA could be regulated by the nature of dyes, the molecular volume, and the end structure of dsDNA. Fluorescence anisotropy ascended with the increased number of base pairs up to 18 bp and leveled off thereafter, indicating the molecular volume was not the only factor responsible for fluorescence anisotropy. By choosing dyes with the positively charged center, high fluorescence anisotropy signal was obtained due to the confinement of the segmental motion of dyes through the electrostatic interaction. By properly designing the end structure of dsDNA, fluorescence anisotropy could be further improved by enlarging the effective overall rotational volume, as supported by two-dimensional (2D) (1)H-(1)H nuclear Overhauser enhancement spectroscopy (NOESY). With the successful enhancement of the fluorescence anisotropy for terminally labeled dsDNA, simple and universal designs were demonstrated by sensing of major classes of analytes from macromolecules (DNA and protein) to small molecules (cocaine).
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Affiliation(s)
- Hongduan Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, ‡Beijing NMR Center, and §College of Life Sciences, Peking University , Beijing, 100871, China
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Jebali A, Hekmatimoghaddam S, Kazemi B, De La Fuente JM. Presentation of a nano-based tag for immunoassay, based on amine-modified bovine serum albumin nanoparticles. IET Nanobiotechnol 2015; 9:43-51. [PMID: 25650325 DOI: 10.1049/iet-nbt.2014.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate four immunoassays, based on amine-modified bovine serum albumin nanoparticles (AMBSANPs). First, the capability of nitrate absorption by AMBSANPs under different conditions was evaluated. Then, serial concentrations of pure βHCG were added to wells coated with βHCG antibody for immunoassays 1 and 2, and wells coated with βHCG aptamer for immunoassays 3 and 4. Next, AMBSANPs conjugated with βHCG antibody was added for immunoassays 1 and 3, and AMBSANPs conjugated with βHCG aptamer were added for immunoassays 2 and 4. Finally, the optical density (OD) of each well was read at 340 nm, and compared with controls. Moreover, the concentration of βHCG in the clinical samples was quantified by immunoassays 1, 2, 3, 4 and ELISA, and then compared. The effect of some serum interferences on these immunoassay methods was evaluated. The authors observed that the amount of nitrate absorption by AMBSANPs increased with an increase in H+ ion concentration and temperature, and decreased with an increase in ion strength. The correlation (R2) between ELISA and immunoassays 1, 2, 3 and 4 were 0.97, 0.97, 0.98, 0.99, respectively. It was found that the increase in the serum interferences led to a decrease in the measured βHCG concentration.
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Affiliation(s)
- Ali Jebali
- Department of Medical Nanotechnology, Pajoohesh Lab, Yazd, Iran
| | - Seyedhossein Hekmatimoghaddam
- Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Bahram Kazemi
- Department of Biotechnology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Jesus Martinez De La Fuente
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication Technology of the Ministry of Education, Research Institute of Translation Medicine, Shanghai Jiao Tong University, Dongchuan Road 800, 200240 Shanghai, People's Republic of China
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40
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Zhang JJ, Cao JT, Shi GF, Huang KJ, Liu YM, Ren SW. A luminol electrochemiluminescence aptasensor based on glucose oxidase modified gold nanoparticles for measurement of platelet-derived growth factor BB. Talanta 2015; 132:65-71. [DOI: 10.1016/j.talanta.2014.08.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 12/21/2022]
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Emahi I, Mulvihill IM, Baum DA. Pyrroloquinoline quinone maintains redox activity when bound to a DNA aptamer. RSC Adv 2015. [DOI: 10.1039/c4ra11052h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Newly identified DNA aptamers for PQQ provide an environment in which PQQ is still accessible for redox chemistry.
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Affiliation(s)
- Ismaila Emahi
- Saint Louis University
- Department of Chemistry
- St. Louis
- USA 63103
| | | | - Dana A. Baum
- Saint Louis University
- Department of Chemistry
- St. Louis
- USA 63103
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42
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Zhen SJ, Yu Y, Li CM, Huang CZ. Graphene oxide amplified fluorescence anisotropy for label-free detection of potassium ion. Analyst 2015; 140:353-7. [DOI: 10.1039/c4an01433b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A label-free fluorescence anisotropy method for the sensitive detection of potassium ion, by using graphene oxide as enhancer, was established.
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Affiliation(s)
- Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- P.R. China
| | - Yan Yu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Sciences
- Southwest University
- P.R. China
| | - Chun Mei Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Sciences
- Southwest University
- P.R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- P.R. China
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Huang Y, Liu X, Shi M, Zhao S, Hu K, Chen ZF, Liang H. Ultrasensitive fluorescence polarization aptasensors based on exonuclease signal amplification and polystyrene nanoparticle amplification. Chem Asian J 2014; 9:2755-60. [PMID: 25081952 DOI: 10.1002/asia.201402563] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Indexed: 11/08/2022]
Abstract
Here, we combine T7 exonuclease (T7 Exo) signal amplification and polystyrene nanoparticle (PS NP) amplification to develop novel fluorescence polarization (FP) aptasensors. The binding of a target/open aptamer hairpin complex or a target/single-stranded aptamer complex to dye-labeled DNA bound to PS NPs, or the self-assembly of two aptamer subunits (one of them labeled with a dye) into a target/aptamer complex on PS NPs leads to the cyclic T7 Exo-catalyzed digestion of the dye-labeled DNA or the dye-labeled aptamer subunit. This results in a substantial decrease in the FP value for the amplified sensing process. Our newly developed aptasensors exhibit a sensitivity five orders of magnitude higher than that of traditional homogeneous aptasensors and a high specificity for the target molecules. These distinct advantages of our proposed assay protocol make it a generic platform for the design of amplified aptasensors for ultrasensitive detection of various target molecules.
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Affiliation(s)
- Yong Huang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004 (China).
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Ouellet E, Lagally ET, Cheung KC, Haynes CA. A simple method for eliminating fixed-region interference of aptamer binding during SELEX. Biotechnol Bioeng 2014; 111:2265-79. [PMID: 24895227 DOI: 10.1002/bit.25294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 01/20/2023]
Abstract
Standard libraries for systematic evolution of ligands by exponential enrichment (SELEX) typically utilize flanking regions that facilitate amplification of aptamers recovered from each selection round. Here, we show that these flanking sequences can bias the selection process, due in part to their ability to interfere with the fold or function of aptamers localized within the random region of the library sequence. We then address this problem by investigating the use of complementary oligonucleotides as a means to block aptamer interference by each flanking region. Isothermal titration calorimetry (ITC) studies are combined with fold predictions to both define the various interference mechanisms and assess the ability of added complementary oligonucleotides to ameliorate them. The proposed blocking strategy is thereby refined and then applied to standard library forms of benchmark aptamers against human α-thrombin, streptavidin, and vascular endothelial growth factor (VEGF). In each case, ITC data show that the new method effectively removes fixed-region mediated interference effects so that the natural binding affinity of the benchmark aptamer is completely restored. We further show that the binding affinities of properly functioning aptamers within a selection library are not affected by the blocking protocol, and that the method can be applied to various common library formats comprised of different flanking region sequences. Finally, we present a rapid and inexpensive qPCR-based method for determining the mean binding affinity of retained aptamer pools and use it to show that introduction of the pre-blocking method into the standard SELEX protocol results in retention of high-affinity aptamers that would otherwise be lost during the first round of selection. Significant enrichment of the available pool of high-affinity aptamers is thereby achieved in the first few rounds of selection. By eliminating single-strand (aptamer-like) structures within or involving the fixed regions, the technique is therefore shown to isolate aptamer sequence and function within the desired random region of the library members, and thereby provide a new selection method that is complementary to other available SELEX protocols.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3; Biomedical Engineering Program, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
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Bi S, Luo B, Ye J, Wang Z. Label-free chemiluminescent aptasensor for platelet-derived growth factor detection based on exonuclease-assisted cascade autocatalytic recycling amplification. Biosens Bioelectron 2014; 62:208-13. [PMID: 25016251 DOI: 10.1016/j.bios.2014.06.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/14/2014] [Accepted: 06/26/2014] [Indexed: 12/11/2022]
Abstract
Here an exonuclease III (Exo III)-assisted cascade autocatalytic recycling amplification (Exo-CARA) strategy is proposed for label-free chemiluminescent (CL) detection of platelet-derived growth factor BB (PDGF-BB) by taking advantage of both recognition property of aptamer and cleavage function of Exo III. Functionally, this system consists of a duplex DNA (aptamer-blocker hybrid), two kinds of hairpin structures (MB1 and MB2), and Exo III. Upon recognizing and binding with PDGF-BB, aptamer folds into a close configuration, which initiates the proposed Exo-CARA reaction (Recyclings I→II→III→II). Finally, numerous "caged" G-quadruplex sequences on DNAzyme1 and DNAzyme2 release that intercalate hemin to catalyze the oxidation of luminol by H2O2 to generate an amplified CL signal, achieving excellent specificity and high sensitivity with a detection limit of 6.8×10(-13) M PDGF-BB. The proposed strategy has the advantages of simple design, isothermal conditions, homogeneous reaction without separation and washing steps, effective-cost without the need of labeling, and high amplification efficiency, which might be a universal and promising protocol for the detection of a variety of biomolecules whose aptamers undergo similar conformational changes.
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Affiliation(s)
- Sai Bi
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, Qingdao University, Qingdao 266071, PR China.
| | - Baoyu Luo
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Jiayan Ye
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Zonghua Wang
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Collaborative Innovation Center for Marine Biomass Fiber Materials and Textiles, Qingdao University, Qingdao 266071, PR China.
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Xiong X, Lv Y, Chen T, Zhang X, Wang K, Tan W. Nucleic acid aptamers for living cell analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:405-426. [PMID: 24896309 DOI: 10.1146/annurev-anchem-071213-015944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as "chemical antibodies," have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.
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Affiliation(s)
- Xiangling Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
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Liu J, Yu J, Chen J, Yang R, Shih K. Signal-amplification and real-time fluorescence anisotropy detection of apyrase by carbon nanoparticle. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 38:206-11. [PMID: 24656370 DOI: 10.1016/j.msec.2014.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/23/2014] [Accepted: 02/04/2014] [Indexed: 11/19/2022]
Abstract
Carbon nanomaterial combined with aptamer has been developed as an efficient bioanalytical method in sensor design. Herein, depending on carbon nanoparticle (cCNP)-enhanced fluorescence anisotropy (FA), a novel aptamer-based sensor (aptasensor) enabling signal-amplification and real-time detection of apyrase is reported. The foundation of our sensor design based on ATP-aptamer(P) can be adsorbed on the surface of cCNPs, resulting in the increase of FA due to the mass of cCNPs, and P-ATP complex has weak binding ability to cCNPs with minimal change of FA. Apyrase, being an integral membrane protein, can hydrolyze ATP and make P-ATP complex disassemble, and thus lead to the increasing of FA. Therefore, this approach is demonstrated to be a novel candidate for the detection of apyrase, with high sensitivity and selectivity. The linear dynamic range for the concentrations of apyrase is between 0.1 and 0.5 U/μL along with a detection limit of 0.05 U/μL. Furthermore, these results indicated that our design is a flexible and sensitive method for biomolecule analysis, which makes it promising for practical biomolecule analyses.
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Affiliation(s)
- Jinhua Liu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China; College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, People's Republic of China.
| | - Jing Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China; College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Jianrong Chen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China; College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Kaimin Shih
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, People's Republic of China.
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Zhang D, Yin L, Meng Z, Yu A, Guo L, Wang H. A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer. Anal Chim Acta 2014; 812:161-7. [PMID: 24491777 DOI: 10.1016/j.aca.2013.12.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/10/2013] [Accepted: 12/24/2013] [Indexed: 12/27/2022]
Abstract
Sensitive and selective detection of Pb(2+) is of great importance to both human health and environmental protection. Here we propose a novel fluorescence anisotropy (FA) approach for sensing Pb(2+) in homogeneous solution by a G-rich thrombin binding aptamer (TBA). The TBA labeled with 6-carboxytetramethylrhodamine (TMR) at the seventh thymine nucleotide was used as a fluorescent probe for signaling Pb(2+). It was found that the aptamer probe had a high FA in the absence of Pb(2+). This is because the rotation of TMR is restricted by intramolecular interaction with the adjacent guanine bases, which results in photoinduced electron transfer (PET). When the aptamer probe binds to Pb(2+) to form G-quadruplex, the intramolecular interaction should be eliminated, resulting in faster rotation of the fluorophore TMR in solution. Therefore, FA of aptamer probe is expected to decrease significantly upon binding to Pb(2+). Indeed, we observed a decrease in FA of aptamer probe upon Pb(2+) binding. Circular dichroism, fluorescence spectra, and fluorescence lifetime measurement were used to verify the reliability and reasonability of the sensing mechanism. By monitoring the FA change of the aptamer probe, we were able to real-time detect binding between the TBA probe and Pb(2+). Moreover, the aptamer probe was exploited as a recognition element for quantification of Pb(2+) in homogeneous solution. The change in FA showed a linear response to Pb(2+) from 10 nM to 2.0 μM, with 1.0 nM limit of detection. In addition, this sensing system exhibited good selectivity for Pb(2+) over other metal ions. The method is simple, quick and inherits the advantages of aptamer and FA.
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Affiliation(s)
- Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | - Lei Yin
- School of Chemical Engineering and Environment, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Zihui Meng
- School of Chemical Engineering and Environment, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing, 100872, PR China
| | - Lianghong Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
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Jin X, Zhao J, Zhang L, Huang Y, Zhao S. An enhanced fluorescence polarization strategy based on multiple protein–DNA–protein structures for sensitive detection of PDGF-BB. RSC Adv 2014. [DOI: 10.1039/c3ra44092c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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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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