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Yuan Z, Xu P, Yu F, Zhang D, Zhao Q, Yu W, Wang H. An electroosmotic flow-free two-direction migration strategy enables fast affinity capillary electrophoresis to study the weak interactions between basic peptides and RNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5833-5838. [PMID: 33227112 DOI: 10.1039/d0ay01515f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Affinity Capillary Electrophoresis (ACE) is a useful analytical tool to study noncovalent interactions. However, it remains challenging for ACE to measure weak and unstable interactions due to the fast dissociation of the binding complex and the possible destruction of the complex by a high electric field. In this study, we proposed a two-direction migration strategy that enables ACE to detect weak and unstable but important interactions by decreasing the migration distance of the binding complex and controlling the opposite migration direction of the free probe. By synthesizing a polyacrylamide-coated neutral capillary, free of electroosmotic flow, two-direction CE migration of basic peptides (positively charged) and peptide-RNA complexes (negatively charged) was achieved. Furthermore, the weak interactions between small nuclear U2 RNA and histone peptides were detected by this two-direction migration CE approach. The effects of the methylation states of histone peptides on the weak peptide-RNA interactions were also explored by this new approach. Collectively, the suggested modification of the ACE method is able to qualitatively characterize weak interactions.
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Affiliation(s)
- Zheng Yuan
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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2
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Zhang Y, Zhu L, He P, Zi F, Hu X, Wang Q. Sensitive assay of Escherichia coli in food samples by microchip capillary electrophoresis based on specific aptamer binding strategy. Talanta 2019; 197:284-290. [PMID: 30771937 DOI: 10.1016/j.talanta.2019.01.040] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 11/30/2022]
Abstract
The rapid and cost-effective detection of bacteria is of great importance to ensuring food safety, preventing food poisoning. Herein, we developed a sensitive detection of Escherichia coli (E. coli) using bacteria-specific aptamer in conjunction with microchip capillary electrophoresis-coupled laser-induced fluorescence (MCE-LIF). Based on the differences between charge to mass ratios of free aptamer and bacteria-aptamer complex, which influence their electrophoretic mobilities, the separation of free aptamers and complex peaks by MCE could be achieved. Under optimal conditions, the sensitive detection of E. coli was achieved with a detection limit of 3.7 × 102 CFU mL-1, at a fast response of 135 s and a short detection length of 2.3 cm. The spiked recovery experiment showed that E. coli could be recovered from spiked drinking water and milk samples with recovery rates of 94.7% and 92.8%, respectively. This work demonstrates that the established detection strategy can be a useful tool for the detection and/or monitoring of E. coli in food and environment.
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Affiliation(s)
- Yan Zhang
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China; School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Luqi Zhu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Futing Zi
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China
| | - Xianzhi Hu
- Faculty of Science, Kunming University of Science and Technology, Kunming 650500, China.
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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3
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Zhang Y, Luo F, Zhang Y, Zhu L, Li Y, Zhao S, He P, Wang Q. A sensitive assay based on specific aptamer binding for the detection of Salmonella enterica serovar Typhimurium in milk samples by microchip capillary electrophoresis. J Chromatogr A 2017; 1534:188-194. [PMID: 29289340 DOI: 10.1016/j.chroma.2017.12.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 11/27/2022]
Abstract
The detection of Salmonella enterica serovar Typhimurium (S. Typhimurium) is very important for the prevention of food poisoning and other infectious diseases. Here we reported a simple and sensitive strategy to test S. Typhimurium by microchip capillary electrophoresis couple with laser-induced fluorescence (MCE-LIF) based on the specific reaction between the bacterium and corresponding aptamers. Based on the differences in charge to mass ratio between bacteria-aptamer complexes and free aptamers, a separation of the complexes and free aptamers could be obtained by MCE. The optimal parameters of the specific reaction including fluorescent dye concentration, Mg2+ concentration, incubation time, and pH of incubation solution were carefully investigated. Meanwhile, a non-specific DNA was exploited as a contrast for the detection of S. Typhimurium. Under the optimal conditions, a rapid separation of the bacteria-aptamer complex and free aptamers was achieved within 135 s with a limit of detection (S/N = 3) of 3.37 × 102 CFU mL-1. This method was applied for the detection of S. Typhimurium in fresh milk samples and a recovery rate of 95.8% was obtained. The experimental results indicated that the specific aptamers are of enough biostability and the established method could be used to analyze S. Typhimurium in foods.
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Affiliation(s)
- Yan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Feifei Luo
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yating Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Luqi Zhu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Yi Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Shuangli Zhao
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
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4
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Bai Y, Li Y, Zhang D, Wang H, Zhao Q. Enhancing the Affinity of Anti-Human α-Thrombin 15-mer DNA Aptamer and Anti-Immunoglobulin E Aptamer by PolyT Extension. Anal Chem 2017; 89:9467-9473. [PMID: 28763192 DOI: 10.1021/acs.analchem.7b02313] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aptamer affinity capillary electrophoresis-laser-induced fluorescence (CE-LIF) for protein detection takes advantage of aptamers for their ease of synthesis and labeling, small size, and having many negative charges. Its success relies on the high binding affinity of aptamers. One 15-mer DNA aptamer (5'-GGT TGG TGT GGT TGG-3', Apt15) shows desirable specificity for human α-thrombin, an important enzyme with multiple functions in blood. However, Apt15 has weak binding affinity, and the use of Apt15 in affinity CE-LIF analysis remains challenging. Here we reported that extension of Apt15 at the 3'-end with a polyT tail having length of 18 T or longer significantly enhanced its affinity and enabled a well-isolated and stable peak for thrombin-aptamer complex in affinity CE. It was likely that the improvement of binding affinity resulted from double binding, an additional interaction of the polyT tail with thrombin in addition to the Apt15 section binding to thrombin. With dye-labeled Apt15 having a T25 tail, we achieved detection of thrombin at concentrations as low as 0.1 nM by affinity CE-LIF. This aptamer probe specifically bound to human α-thrombin, showing negligible affinity for human β- and γ-thrombin, which are proteolyzed derivatives of human alpha α-thrombin and share similar structure. This strategy of adding a polyT extension also enhanced the binding affinity of anti-immunoglobulin E aptamer in CE-LIF analysis, showing that the affinity enhancement approach is not limited to the thrombin-binding aptamer and has potential for more applications in bioanalysis.
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Affiliation(s)
- Yunlong Bai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China.,Institute of Environmental Science, Shanxi University , Taiyuan 030006, China
| | - Yapiao Li
- 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
| | - Dapeng Zhang
- 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
| | - 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
| | - 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
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Aeksiri N, Warakulwit C, Hannongbua S, Unajak S, Choowongkomon K. Use of Capillary Electrophoresis to Study the Binding Interaction of Aptamers with Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT : Studying the Binding Interaction of Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT with Aptamers by Performing the Capillary Electrophoresis. Appl Biochem Biotechnol 2016; 182:546-558. [PMID: 27900665 DOI: 10.1007/s12010-016-2343-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022]
Abstract
A number of nucleic acid aptamers with high affinities to human immunodeficiency virus reverse transcriptase (HIV-1 RT) are currently known. They can potentially be developed as broad-spectrum antiviral drugs, but there is little known about their binding interaction with mutant HIV-1 RT. Therefore, we utilized non-equilibrium capillary electrophoresis of equilibrium mixture (NECEEM) to study the interaction of three HIV-1 RTs (wild type, K103N, and double mutant (K103N/Y181C)) with RT1t49 and RT12 aptamers. This approach was used to study and evaluate the K d values of these molecules. The results showed that the K d values of the tested aptamers were lower than that of the DNA substrate. The results also pointed out that RT1t49 could bind with all HIV-1 RTs and compete with the DNA substrate at the active site. Moreover, we studied the binding stoichiometry of HIV-1 RT using aptamers as probes. The findings showed evidence of two binding stoichiometries with HIV-1 RT and the RT12 aptamer but only one binding stoichiometry for RT1t49. In addition, RT1t49 could bind specifically with the wild-type, K103N, and double mutants in Escherichia coli lysate. This result also indicated that the aptamer could detect HIV-1 RT in the presence of E. coli lysate.
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Affiliation(s)
- Niran Aeksiri
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chompunuch Warakulwit
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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6
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Affinity capillary electrophoresis with laser induced fluorescence detection for thrombin analysis using nuclease-resistant RNA aptamers. J Chromatogr A 2016; 1476:124-129. [PMID: 27855943 DOI: 10.1016/j.chroma.2016.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/30/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
Aptamer affinity capillary electrophoresis coupled with laser-induced fluorescence (CE-LIF) combines the advantages of affinity aptamer, rapid CE separation, and high sensitivity detection. Here we reported an affinity CE-LIF assay for thrombin by using a fluorophore-labeled RNA aptamer containing 2'-fluoro modification in sugar rings of pyrimidine nucleotides (C and U) as affinity ligand. This RNA aptamer has high binding affinity, specificity and biostability. Thrombin at 0.2nM was successfully detected. This RNA aptamer allowed for the detection of thrombin spiked in diluted human serum sample due to the nuclease resistance. The RNA aptamer has comparable binding affinity to a 29-mer DNA aptamer for thrombin, and the binding site of the RNA aptamer on thrombin partially overlaps with the binding site of the 29-mer DNA aptamer on thrombin. It shows the nuclease-resistant RNA aptamers are promising in assays for thrombin.
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7
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Li C, Wang H. Selective enzymatic cleavage and labeling for sensitive capillary electrophoresis laser-induced fluorescence analysis of oxidized DNA bases. J Chromatogr A 2015; 1406:324-30. [DOI: 10.1016/j.chroma.2015.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/04/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022]
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8
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Liu S, Zhang D, Wang H. Transient isotachophoresis focusing of DNA and DNA-protein complexes is essentially enhanced by spontaneously dissolved aerial carbon dioxide in electrolytes. Anal Chem 2015; 87:554-60. [PMID: 25437902 DOI: 10.1021/ac504173b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of a highly adapted high-E zone is critical to isotachophoresis separation and focusing. Recently, we discovered that the high-E zone is present only in a small portion of electrophoresis channel in the presence of EOF (Liu, S. Q. et al. J. Am. Chem. Soc. 2013, 135, 4644-4647). Accordingly, a much narrower high-E zone is presumably present in t-ITP. If so, it is hard to achieve efficient t-ITP focusing. Indeed, by online coupling t-ITP with CE-LIF immunoassay, the immunocomplexes of carcinogenic BPDE-dG adducts are not efficiently focused using a freshly prepared background electrolyte. Intriguingly, we observed that 20-day stored background electrolyte displays a 10-fold better focusing efficiency. We hypothesize that the unexpected phenomenon is associated with the dissolution of aerial carbon dioxide, which is mainly converted to ionic HCO3(-) in the weak alkaline background electrolyte. Consequently, HCO3(-) of high electrophoretic mobility will be continuously injected into the capillary along with the background electrolyte and act as an alternative leading ion to improve the focusing. By addition of dry ice (without causing significant pH decrease, ΔpH < 0.4) to freshly prepared background electrolytes, we immediately observed the enhanced focusing of immunocomplexes of the DNA adducts. NH4HCO3 and Na2CO3, included in the background electrolyte, also improve the focusing efficiency and reproducibility. All these consistently support our hypothesis. To understand the underlying mechanism, an advanced CE-SMFI was exploited to monitor in real time the motion of single DNA molecules and the E change throughout t-ITP. We uncovered that t-ITP can induce a local high-E zone, but the presence of HCO3(-) in the background electrolyte could greatly increase the E value in the high-E zone, which allows more DNA molecules to rapidly move backward and to be efficiently stacked at LE/TE boundary. This study provides new insight into nonuniform electric field-induced electrophoresis focusing.
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Affiliation(s)
- Shengquan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , ShuangQing Road 18, Beijing 100085, China
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Zou D, Zhang D, Liu S, Zhao B, Wang H. Interplay of binding stoichiometry and recognition specificity for the interaction of MBD2b protein and methylated DNA revealed by affinity capillary electrophoresis coupled with laser-induced fluorescence analysis. Anal Chem 2014; 86:1775-82. [PMID: 24422445 DOI: 10.1021/ac4036636] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The methyl-CpG binding domain (MBD) family proteins can specifically bind methylated DNA sequences and thereby mediate gene transcription. In this study, we used neutral capillary electrophoresis coupled with laser-induced fluorescence to investigate the interactions of DNA and MBD2b, a model MBD family protein with the highest affinity. For this purpose, we synthesized 13 double-stranded oligonucleotides of varying length (20 bp to 80 bp) and of varying methylation density. The sequences of these oligonucleotides were adapted from a frequently methylated promoter region of human p16(INK4a) gene. We demonstrate that multiple MBD2b proteins can bind to one DNA molecule with a DNA length-dependent binding stoichiometry. Each MBD2b protein can occupy 20 nucleotides in a bound DNA molecule regardless of the methylation status of DNA. By binding multiple MBD2b proteins (up to four protein molecules) to one dsDNA molecule (80 bp), methylated and unmethylated DNA were bound at similar percentages. Although the total amount of the DNA-MBD2b complexes increases with increasing DNA length for both unmethylated and methylated DNA, the DNA-MBD2b complexes of 1:1 display more than 10-fold higher affinity for methylated DNA (e.g., 40 bp DNA) accompanying a 20-fold lower dissociation rate constant. Hence, our study clarifies for the first time that the specificity of MBD2b to methylated DNA decreases as more MBD2b monomers binding to the same region of DNA. Additionally, this study opens a new venue to improve MBD protein-based assays for detecting DNA methylation.
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Affiliation(s)
- Dandan Zou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 China
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Šmuc T, Ahn IY, Ulrich H. Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics. J Pharm Biomed Anal 2013; 81-82:210-7. [PMID: 23666257 DOI: 10.1016/j.jpba.2013.03.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/11/2013] [Accepted: 03/20/2013] [Indexed: 02/07/2023]
Abstract
Aptamers are small nucleic acid molecules capable of binding to a wide range of target molecules with high affinity and specificity. They have been developed and widely used not only as research tools, but also as biosensors, specific antagonists, and diagnostic markers and as protein purification platform for many pharmaceutical and clinical applications. Here, in this paper we will explore biochemical aspects of aptamer-target interactions and show why aptamers rival antibodies in target recognition and purification procedures. This review will focus on strategies of using aptamers as affinity ligands for molecules of therapeutic and pharmaceutical interest including applications in chromatography and capillary electrophoresis for protein and small molecule purification. Moreover, we will also discuss aptamers whose binding parameters can be controlled on demand for diagnostic approaches and used as sensitive receptors in biosensorics. Aptamers have opened up exciting fields in basic and applied research of pharmaceutical and biotechnological interest.
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Affiliation(s)
- Tina Šmuc
- Laboratory for Bio-instrumentation, Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
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Cheow LF, Han J. Continuous signal enhancement for sensitive aptamer affinity probe electrophoresis assay using electrokinetic concentration. Anal Chem 2011; 83:7086-93. [PMID: 21809885 PMCID: PMC3179849 DOI: 10.1021/ac201307d] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe an electrokinetic concentration-enhanced aptamer affinity probe electrophoresis assay to achieve highly sensitive and quantitative detection of protein targets in a microfluidic device. The key weaknesses of aptamer as a binding agent (weak binding strength/fast target dissociation) were counteracted by continuous injection of fresh sample while band-broadening phenomena were minimized due to self-focusing effects. With 30 min of continuous signal enhancement, we can detect 4.4 pM human immunoglobulin E (IgE) and 9 pM human immunodeficiency virus 1 reverse transcriptase (HIV-1 RT), which are among the lowest limits of detection (LOD) reported. IgE was detected in serum sample with a LOD of 39 pM due to nonspecific interactions between aptamers and serum proteins. The method presented in this paper also has broad applicability to improve sensitivities of various other mobility shift assays.
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Affiliation(s)
- Lih Feng Cheow
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Zhu Z, Ravelet C, Perrier S, Guieu V, Roy B, Perigaud C, Peyrin E. Multiplexed detection of small analytes by structure-switching aptamer-based capillary electrophoresis. Anal Chem 2010; 82:4613-20. [PMID: 20446673 DOI: 10.1021/ac100755q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Affinity probe capillary electrophoresis (APCE) assays, combining the separation power of CE with the specificity of interactions occurring between a target and a molecular recognition element (MRE), have become important analytical tools in many application fields. In this report, a rationalized strategy, derived from the structure-switching aptamer concept, is described for the design of a novel APCE mode dedicated to small molecule detection. Two assay configurations were reported. The first one, developed for the single-analyte determination, was based on the use of a cholesteryl-tagged aptamer (Chol-Apt) as the MRE and its fluorescein-labeled complementary strand (CS*) as the tracer (laser-induced fluorescence detection). Under micellar electrokinetic chromatography (MEKC) conditions, free CS* and the hybrid formed with Chol-Apt (duplex*) were efficiently separated (and then quantified) through the specific shift of the electrophoretic mobility of the cholesteryl-tagged species in the presence of a neutral micellar phase. When the target was introduced into the preincubated sample, the hybridized form was destabilized, resulting in a decrease in the duplex* peak area and a concomitant increase in the free CS* peak area. The second format, especially designed for multianalyte sensing, employed dually cholesteryl- and fluorescein-labeled complementary strands (Chol-CS*) of different lengths and unmodified aptamers (Apt). The size-dependent electrophoretic separation of different Chol-CS* forms from each other and from their corresponding duplexes* was also accomplished under MEKC conditions. The simultaneous detection of multiple analytes in a single capillary was performed by monitoring accurately each target-induced duplex-to-complex change. This method could expand significantly the potential of small solute APCE analysis in terms of simplicity, adaptability, generalizability, and high-throughput analysis capability.
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Affiliation(s)
- Zhenyu Zhu
- Departement de Pharmacochimie Moléculaire, UMR 5063 CNRS, ICMG FR 2607, Université Grenoble I, Campus universitaire, Saint-Martin d'Hères, France
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13
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MENG Q, GUO L, SHEN R, XIE J. A novel capillary electrophoretic method for protein determination using bicinchoninic acid-Cu +colorimetric reaction. Se Pu 2010; 28:682-7. [DOI: 10.3724/sp.j.1123.2010.00682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Wang C, Li T, Wang Z, Feng F, Wang H. Quantitative study of stereospecific binding of monoclonal antibody to anti-benzo(a)pyrene diol epoxide-N2-dG adducts by capillary electrophoresis immunoassay. J Chromatogr A 2010; 1217:2254-61. [DOI: 10.1016/j.chroma.2010.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 02/03/2010] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
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15
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Zhang H, Li XF, Le XC. Differentiation and detection of PDGF isomers and their receptors by tunable aptamer capillary electrophoresis. Anal Chem 2009; 81:7795-800. [PMID: 19691297 DOI: 10.1021/ac901471w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tunable aptamer capillary electrophoresis (CE) techniques were developed to enable the separation and detection of platelet derived growth factor (PDGF) isomers and their receptors. Using an aptamer that formed a stable complex with the B chain but not with the A chain of PDGF, we were able to tweak the electrophoretic mobilities of the PDGF isomers for their separation. PDGF-AB bound to a single aptamer molecule was well resolved from PDGF-BB bound to two aptamer molecules. Simultaneous determination of 50 pM of two isomers was accomplished in a single analysis. Furthermore, PDGF-AB was used as a connector to bring receptor alpha and fluorescent aptamer into a single complex molecule. As a result, the formation of a (receptor alpha)-(PDGF-AB)-(fluorescent aptamer) ternary complex enabled the detection of the receptor alpha by tunable aptamer CE. A competitive assay was developed to determine receptor beta, making use of the competition between the receptor beta and fluorescent aptamer in binding to PDGF-BB. Detection limits were 0.5 nM for PDGF receptor alpha and 3 nM for receptor beta. Determination of PDGF isomers and their receptors in diluted serum samples showed no interference from the sample matrix.
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Affiliation(s)
- Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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16
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Wang Z, Lu M, Wang X, Yin R, Song Y, Le XC, Wang H. Quantum Dots Enhanced Ultrasensitive Detection of DNA Adducts. Anal Chem 2009; 81:10285-9. [DOI: 10.1021/ac9021105] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhixin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - Meiling Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - Xiaoli Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - Ruichuan Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - Yuling Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - X. Chris Le
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3, AB, Canada
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Stratis-Cullum DN, McMasters S, Pellegrino PM. Evaluation of Relative Aptamer Binding toCampylobacter jejuniBacteria Using Affinity Probe Capillary Electrophoresis. ANAL LETT 2009. [DOI: 10.1080/00032710903137376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Wang X, Song Y, Song M, Wang Z, Li T, Wang H. Fluorescence Polarization Combined Capillary Electrophoresis Immunoassay for the Sensitive Detection of Genomic DNA Methylation. Anal Chem 2009; 81:7885-91. [DOI: 10.1021/ac901681k] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaoli Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
| | - Yuling Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
| | - Zhixin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
| | - Tao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China, 100085
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19
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DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway. Proc Natl Acad Sci U S A 2009; 106:12849-54. [PMID: 19549864 DOI: 10.1073/pnas.0902281106] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Localized DNA melting may provide a general strategy for recognition of the wide array of chemically and structurally diverse DNA lesions repaired by the nucleotide excision repair (NER) pathway. However, it is not clear what causes such DNA melting and how it is driven. Here, we show a DNA wrapping-melting model supported by results from dynamic monitoring of the key DNA-protein and protein-protein interactions involved in the early stages of the Escherichia coli NER process. Using an analytical technique involving capillary electrophoresis coupled with laser-induced fluorescence polarization, which combines a mobility shift assay with conformational analysis, we demonstrate that DNA wrapping around UvrB, mediated by UvrA, is an early event in the damage-recognition process during E. coli NER. DNA wrapping of UvrB was confirmed by Förster resonance energy transfer and fluorescence lifetime measurements. This wrapping did not occur with readily denaturable damaged DNA substrates ("bubble" DNA), suggesting that DNA wrapping of UvrB plays an important role in the induction of DNA melting around the damage site. Analysis of DNA wrapping of mutant UvrB Y96A further suggests that a cooperative interaction between DNA wrapping of UvrA(2)B and contact of the beta-hairpin of UvrB with the bulky damage moiety may be involved in the local DNA melting at the damage site.
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20
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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21
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Wang C, Feng F, Wang Z, Li T, Le XC, Wang H. Synthesis and Characterization of DNA Fluorescent Probes Containing a Single Site-Specific Stereoisomer of anti-Benzo[a]pyrene Diol Epoxide-N2-dG. Chem Res Toxicol 2009; 22:676-82. [DOI: 10.1021/tx800419p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chao Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Feng Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Zhixin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Tao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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22
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Liu J, Liu Z, Kang M, Liu S, Chen HY. Combination of large volume sample stacking and reversed pH junction in capillary electrophoresis for online preconcentration of glycoforms of recombinant human erythropoietin. J Sep Sci 2009; 32:422-9. [DOI: 10.1002/jssc.200800387] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Li T, Wang H. Organic Osmolyte Mediated Kinetic Capillary Electrophoresis for Study of Protein−DNA Interactions. Anal Chem 2009; 81:1988-95. [DOI: 10.1021/ac8025256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Environmental Chemistry and Eco-Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Eco-Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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24
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Giovannoli C, Baggiani C, Anfossi L, Giraudi G. Aptamers and molecularly imprinted polymers as artificial biomimetic receptors in affinity capillary electrophoresis and electrochromatography. Electrophoresis 2008; 29:3349-65. [PMID: 18646281 DOI: 10.1002/elps.200800004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Artificial biomimetic receptors, such as aptamers and molecular-imprinted polymers, show antibody-like properties which are due to molecular recognition phenomena characterized by high affinity and selectivity. These binding features have made them suitable in all those application fields in which selective recognition is required. Thus, it is not surprising that they are finding applications in affinity CE as well. Recently, a variety of ACE methods have shown themselves to be suitable tools to provide a detailed quantitative characterization of the thermodynamic and kinetic aspects of binding. At the same time, affinity CE can exploit the peculiarities of these binding interactions to set up CE-based analytical tools for the separation and the determination of specific target molecules in microscale formats. This review will provide a detailed description of affinity CE methods recently reported in the literature and related to these topics.
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Affiliation(s)
- Cristina Giovannoli
- Department of Analytical Chemistry, University of Torino, Via Giuria 5, Torino, Italy.
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25
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Wang Z, Wang C, Yin J, Li T, Song M, Lu M, Wang H. Focusing and stabilization of bis-intercalating dye-DNA complexes for high-sensitive CE-LIF DNA analysis. Electrophoresis 2008; 29:4454-62. [DOI: 10.1002/elps.200800230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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A electrochemiluminescence aptasensor for detection of thrombin incorporating the capture aptamer labeled with gold nanoparticles immobilized onto the thio-silanized ITO electrode. Anal Chim Acta 2008. [DOI: 10.1016/j.aca.2008.08.041] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Yang Y, Zhang J, Zhou D, Bao JJ. WITHDRAWN: An improved direct pumping approach to eliminate sample bias in capillary electrokinetic injection. Electrophoresis 2007; 30. [PMID: 17351890 DOI: 10.1002/elps.200600387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The EOF pump was successfully used as a means of introducing samples into a capillary system. An improved sample injection device has been developed using a Teflontrade mark union (TU) to link the two capillaries together. The capillary applied high voltage served as the EOF pump to pull the liquid inside while the other one served the purposes of isolating the electric field. Using the bias degree (BD) and SD of bias (SDB), it was possible to quantitatively determine the sampling bias and evaluate the effectiveness of injection approaches in bias elimination. Several related factors were evaluated, and it was found that TU approach could fully eliminate the bias under the optimal conditions. The fracture did not affect the efficiency, leak, or dilute the sample significantly. This approach was effective under both normal and reverse EOF situations and adapted to real samples. Finally, a TU method using grounded injection electrode was proposed and shown to be suitable for samples with low conductivity and high injection voltage.
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Affiliation(s)
- Yan Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P. R. China
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28
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Ravelet C, Grosset C, Peyrin E. Liquid chromatography, electrochromatography and capillary electrophoresis applications of DNA and RNA aptamers. J Chromatogr A 2006; 1117:1-10. [PMID: 16647074 DOI: 10.1016/j.chroma.2006.03.101] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 03/09/2006] [Accepted: 03/21/2006] [Indexed: 10/24/2022]
Abstract
The development of the systematic evolution of ligands by exponential enrichment (SELEX) process has allowed the isolation of oligonucleotide sequences (referred as aptamers) with the capacity to recognize various classes of target molecules with high affinity and specificity. At the present time, various analytical aptamer-based formats have been developed as suitable tools for the detection and quantification of numerous targets, possessing many potential advantages over the most popular antibody technology. In this review, the aptamer applicability to the separation, purification and quantification of various analytes by liquid chromatography, capillary electrophoresis and electrochromatography is addressed.
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Affiliation(s)
- Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, Institut de Chimie Moléculaire de Grenoble FR 2607, Université Joseph Fourier, UFR de Pharmacie de Grenoble, Avenue de Verdun, 38240 Meylan, France
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29
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Auld D, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2005. [DOI: 10.1089/adt.2005.3.439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- National Institutes of Health, Bethesda, MD
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