1
|
Bottari F, Daems E, de Vries AM, Van Wielendaele P, Trashin S, Blust R, Sobott F, Madder A, Martins JC, De Wael K. Do Aptamers Always Bind? The Need for a Multifaceted Analytical Approach When Demonstrating Binding Affinity between Aptamer and Low Molecular Weight Compounds. J Am Chem Soc 2020; 142:19622-19630. [DOI: 10.1021/jacs.0c08691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabio Bottari
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Elise Daems
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
| | - Anne-Mare de Vries
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Stanislav Trashin
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Ronny Blust
- Sphere Research Group, Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Frank Sobott
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - José C. Martins
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Karolien De Wael
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| |
Collapse
|
2
|
Miyagawa A, Okada Y, Okada T. Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field. ACS OMEGA 2020; 5:3542-3549. [PMID: 32118169 PMCID: PMC7045491 DOI: 10.1021/acsomega.9b03860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.
Collapse
|
3
|
Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based immunoassay and aptamer assay: A review. Electrophoresis 2020; 41:414-433. [PMID: 31975407 DOI: 10.1002/elps.201900426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.
Collapse
Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Eble JA. Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction. J Vis Exp 2018. [PMID: 29553569 DOI: 10.3791/57334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The dissociation constant describes the interaction between two partners in the binding equilibrium and is a measure of their affinity. It is a crucial parameter to compare different ligands, e.g., competitive inhibitors, protein isoforms and mutants, for their binding strength to a binding partner. Dissociation constants are determined by plotting concentrations of bound versus free ligand as binding curves. In contrast, titration curves, in which a signal that is proportional to the concentration of bound ligand is plotted against the total concentration of added ligand, are much easier to record. The signal can be detected spectroscopically and by enzyme-linked immunosorbent assay (ELISA). This is exemplified in a protocol for a titration ELISA that measures the binding of the snake venom-derived rhodocetin to its immobilized target domain of α2β1 integrin. Titration ELISAs are versatile and widely used. Any pair of interacting proteins can be used as immobilized receptor and soluble ligand, provided that both proteins are pure, and their concentrations are known. The difficulty so far has been to determine the dissociation constant from a titration curve. In this study, a mathematical function underlying titration curves is introduced. Without any error-prone graphical estimation of a saturation yield, this algorithm allows processing of the raw data (signal intensities at different concentrations of added ligand) directly by mathematical evaluation via non-linear regression. Thus, several titration curves can be recorded simultaneously and transformed into a set of characteristic parameters, among them the dissociation constant and the concentration of binding-active receptor, and they can be evaluated statistically. When combined with this algorithm, titration ELISAs gain the advantage of directly presenting the dissociation constant. Therefore, they may be used more efficiently in the future.
Collapse
Affiliation(s)
- Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster;
| |
Collapse
|
6
|
Mears KS, Markus DL, Ogunjimi O, Whelan RJ. Experimental and mathematical evidence that thrombin-binding aptamers form a 1 aptamer:2 protein complex. APTAMERS (OXFORD, ENGLAND) 2018; 2:64-73. [PMID: 34414355 PMCID: PMC8372783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The thrombin-binding 15mer and 29mer ssDNA aptamers are a widely used model system. Despite their ubiquity, controversies persist regarding the nature of the aptamer-protein interactions. Reported affinities vary widely; the role of metal ions in binding is unclear; the structure of the complex is contested. We interrogated the effects of instrument, buffer, and mathematical model on apparent affinities of thrombin aptamers for their target. Instrumental method had a pronounced effect on affinity constants for the 15mer and marginal effect the apparent affinity of the 29mer. Buffer composition and ionic environment did not have significant effects. Affinity probe capillary electrophoresis experiments revealed distinct peaks from samples of 29mer aptamer and thrombin, supporting the model of a 1 aptamer:2 protein complex. Fits to high quality data with five mathematical models further support this stoichiometry, as the binding of both aptamers was best described by the Hill equation with Hill coefficients > 1. Our results indicate that the instrumental method and mathematical model influence apparent affinity of thrombin aptamers and that both aptamers bind thrombin in a 1 aptamer: 2 protein stoichiometry through an induced fit mechanism.
Collapse
Affiliation(s)
- Kepler S Mears
- Department of Chemistry and Biochemistry, Oberlin College, USA
| | - Daniel L Markus
- Department of Chemistry and Biochemistry, Oberlin College, USA
| | | | - Rebecca J Whelan
- Department of Chemistry and Biochemistry, Oberlin College, USA,Department of Chemistry and Biochemistry, University of Notre Dame, USA,Correspondence to: Rebecca Whelan, , Tel: +574-631-1853, Fax: 574-631-6652
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Guzman NA, Guzman DE. An emerging micro-scale immuno-analytical diagnostic tool to see the unseen. Holding promise for precision medicine and P4 medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:14-29. [DOI: 10.1016/j.jchromb.2015.11.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 01/10/2023]
|
9
|
Microfluidic chip-based silver nanoparticles aptasensor for colorimetric detection of thrombin. Talanta 2015; 150:81-7. [PMID: 26838384 DOI: 10.1016/j.talanta.2015.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/03/2015] [Accepted: 09/06/2015] [Indexed: 12/21/2022]
Abstract
In this paper, a colorimetric silver nanoparticles aptasensor (aptamer-AgNPs) was developed for simple and straightforward detection of protein in microfluidic chip. Surface-functionalized microfluidic channels were employed as the capture platform. Then the mixture of target protein and aptamer-AgNPs were injected into the microfluidic channels for colorimetric detection. To demonstrate the performance of this detection platform, thrombin was chosen as a model target protein. Introduction of thrombin could form a sandwich-type complex involving immobilized AgNPs. The amount of aptamer-AgNPs on the complex augmented along with the increase of the thrombin concentration causing different color change that can be analyzed both by naked eyes and a flatbed scanner. This method is featured with low sample consumption, simple processes of microfluidic platform and straightforward colorimetric detection with aptamer-AgNPs. Thrombin at concentrations as low as 20pM can be detected using this aptasensor without signal amplification. This work demonstrated that it had good selectivity over other proteins and it could be a useful strategy to detect other targets with two affinity binding sites for ligands as well.
Collapse
|
10
|
McKeague M, De Girolamo A, Valenzano S, Pascale M, Ruscito A, Velu R, Frost NR, Hill K, Smith M, McConnell EM, DeRosa MC. Comprehensive analytical comparison of strategies used for small molecule aptamer evaluation. Anal Chem 2015; 87:8608-12. [PMID: 26192270 DOI: 10.1021/acs.analchem.5b02102] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are versatile molecular recognition agents that bind to their targets with high selectivity and affinity. The past few years have seen a dramatic increase in aptamer development and interest for diagnostic and therapeutic applications. As the applications for aptamers expand, the need for a more standardized, stringent, and informative characterization and validation methodology increases. Here we performed a comprehensive analysis of a panel of conventional affinity binding assays using a suite of aptamers for the small molecule target ochratoxin A (OTA). Our results highlight inconsistency between conventional affinity assays and the need for multiple characterization strategies. To mitigate some of the challenges revealed in our head-to-head comparison of aptamer binding assays, we further developed and evaluated a set of novel strategies that facilitate efficient screening and characterization of aptamers in solution. Finally, we provide a workflow that permits rapid and robust screening, characterization, and functional verification of aptamers thus improving their development and integration into novel applications.
Collapse
Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University , 443 Via Ortega, Stanford, California 94305, United States
| | - Annalisa De Girolamo
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Stefania Valenzano
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Michelangelo Pascale
- Institute of Sciences of Food Production, National Research Council of Italy , via G. Amendola 122/O, 70126 Bari, Italy
| | - Annamaria Ruscito
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Ranganathan Velu
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Nadine R Frost
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Kayla Hill
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - McKenzie Smith
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Erin M McConnell
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - Maria C DeRosa
- Chemistry Department, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| |
Collapse
|
11
|
Pagaduan JV, Ramsden M, O'Neill K, Woolley AT. Microchip immunoaffinity electrophoresis of antibody-thymidine kinase 1 complex. Electrophoresis 2015; 36:813-7. [PMID: 25486911 PMCID: PMC4346389 DOI: 10.1002/elps.201400436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/12/2014] [Accepted: 11/27/2014] [Indexed: 11/12/2022]
Abstract
Thymidine kinase 1 (TK1) is an important cancer biomarker whose serum levels are elevated in early cancer development. We developed a microchip electrophoresis immunoaffinity assay to measure recombinant purified TK1 (pTK1) using an antibody (Ab) that binds to human TK1. We fabricated PMMA microfluidic devices to test the feasibility of detecting Ab-pTK1 immune complexes as a step toward TK1 analysis in clinical serum samples. We were able to separate immune complexes from unbound Abs using 0.5× PBS (pH 7.4) containing 0.01% Tween-20, with 1% w/v methylcellulose that acts as a dynamic surface coating and sieving matrix. Separation of the Ab and Ab-pTK1 complex was observed within a 5 mm effective separation length. This method of detecting pTK1 is easy to perform, requires only a 10 μL sample volume, and takes just 1 min for separation.
Collapse
Affiliation(s)
- Jayson V Pagaduan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | | | | | | |
Collapse
|
12
|
Van Meervelt V, Soskine M, Maglia G. Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore. ACS NANO 2014; 8:12826-35. [PMID: 25493908 PMCID: PMC4410316 DOI: 10.1021/nn506077e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we showed that folded proteins can be internalized inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalization of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores can be used to probe conformational heterogeneity in protein:DNA interactions.
Collapse
Affiliation(s)
| | - Misha Soskine
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
| | - Giovanni Maglia
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, the Netherlands
| |
Collapse
|
13
|
Deng B, Lin Y, Wang C, Li F, Wang Z, Zhang H, Li XF, Le XC. Aptamer binding assays for proteins: the thrombin example--a review. Anal Chim Acta 2014; 837:1-15. [PMID: 25000852 DOI: 10.1016/j.aca.2014.04.055] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/26/2014] [Accepted: 04/28/2014] [Indexed: 12/14/2022]
Abstract
Experimentally selected single-stranded DNA and RNA aptamers are able to bind to specific target molecules with high affinity and specificity. Many analytical methods make use of affinity binding between the specific targets and their aptamers. In the development of these methods, thrombin is the most frequently used target molecule to demonstrate the proof-of-principle. This paper critically reviews more than one hundred assays that are based on aptamer binding to thrombin. This review focuses on homogeneous binding assays, electrochemical aptasensors, and affinity separation techniques. The emphasis of this review is placed on understanding the principles and unique features of the assays. The principles of most assays for thrombin are applicable to the determination of other molecular targets.
Collapse
Affiliation(s)
- Bin Deng
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Yanwen Lin
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Chuan Wang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Feng Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Zhixin Wang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - Xing-Fang Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, T6G 2G3, Canada; Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| |
Collapse
|
14
|
Pan Y, Karns K, Herr AE. Microfluidic electrophoretic mobility shift assays for quantitative biochemical analysis. Electrophoresis 2014; 35:2078-90. [PMID: 24591076 DOI: 10.1002/elps.201300500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/31/2014] [Accepted: 02/09/2014] [Indexed: 02/02/2023]
Abstract
Electrophoretic mobility shift assays (EMSAs) play an important role in analytical chemistry, quantitative bioscience, and point-of-care diagnostics. Emerging microfluidic lab-on-a-chip technologies bring high throughput and multiplexed analysis to affinity-based electrophoretic separations, greatly advancing the performance of traditional EMSAs. This review elaborates on the relevant theoretical basis for EMSAs, surveys microfluidic-based EMSA applications in molecular conformation analyses, immunoassays, affinity assays and genomics, and outlines challenges and potential future improvements needed from this powerful assay.
Collapse
Affiliation(s)
- Yuchen Pan
- Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, CA, USA
| | | | | |
Collapse
|
15
|
Xu Y, Redweik S, El-Hady DA, Albishri HM, Preu L, Wätzig H. Precise, fast, and flexible determination of protein interactions by affinity capillary electrophoresis: part 3: anions. Electrophoresis 2014; 35:2203-12. [PMID: 24436007 DOI: 10.1002/elps.201300387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/11/2013] [Accepted: 12/19/2013] [Indexed: 11/09/2022]
Abstract
The binding of physiologically anionic species or negatively charged drug molecules to proteins is of great importance in biochemistry and medicine. Since affinity capillary electrophoresis (ACE) has already proven to be a suitable analytical tool to study the influence of ions on proteins, this technique was applied here for comprehensively studying the influence of various anions on proteins of BSA, β-lactoglobulin, ovalbumin, myoglobin, and lysozyme. The analysis was performed using different selected anions of succinate, glutamate, phosphate, acetate, nitrate, iodide, thiocyanate, and pharmaceuticals (salicylic acid, aspirin, and ibuprofen) that exist in the anionic form at physiological pH 7.4. Due to the excellent repeatability and precision of the ACE measurements, not necessarily strong but significant influences of the anions on the proteins were found in many cases. Different influences in the observed bindings indicated change of charge, mass, or conformational changes of the proteins due to the binding with the studied anions. Combining the mobility-shift and pre-equilibrium ACE modes, rapidity and reversibility of the protein-anion bindings were discussed. Further, circular dichroism has been used as an orthogonal approach to characterize the interactions between the studied proteins and anions to confirm the ACE results. Since phosphate and various anions from amino acids and small organic acids such as succinate or acetate are present in very high concentrations in the cellular environment, even weak influences are certainly relevant as well.
Collapse
Affiliation(s)
- Yuanhong Xu
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Beethovenstr, Braunschweig, Germany; Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | | | | | | | | | | |
Collapse
|
16
|
Chen FY, Wang Z, Li P, Lian HZ, Chen HY. Aptamer-based thrombin assay on microfluidic platform. Electrophoresis 2013; 34:3260-6. [PMID: 24127412 DOI: 10.1002/elps.201300338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/13/2013] [Accepted: 09/22/2013] [Indexed: 11/08/2022]
Abstract
A facile and sensitive aptamer-based protocol has been developed for protein assay on microfluidic platform with fluorescence detection using an off-chip microarray scanner. Aptamer-functionalized magnetic beads were used to capture thrombin that binds to a second aptamer fluorescently labeled by Cy3. Experimental conditions, such as incubation time and temperature, washing time, interfering proteins, and aptamer, etc., were optimized for the microchip method. This work demonstrated there was a good relationship between fluorescence intensity and thrombin concentration in the range of 65-1000 ng/mL with the RSD less than 8%. Notably, an analysis only needs 1 μL volume of sample injection and this system can capture extremely tiny amount thrombin (0.4 fmol). This method has been successfully applied to assay of thrombin in human serum with the recovery of 79.74-95.94%.
Collapse
Affiliation(s)
- Fang-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing, P. R. China
| | | | | | | | | |
Collapse
|
17
|
Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J Am Chem Soc 2012; 134:2781-7. [PMID: 22229655 PMCID: PMC3278221 DOI: 10.1021/ja2105653] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Protein nanopores have been used as stochastic sensors
for the
detection of analytes that range from small molecules to proteins.
In this approach, individual analyte molecules modulate the ionic
current flowing through a single nanopore. Here, a new type of stochastic
sensor based on an αHL pore modified with an aptamer is described.
The aptamer is bound to the pore by hybridization to an oligonucleotide
that is attached covalently through a disulfide bond to a single cysteine
residue near a mouth of the pore. We show that the binding of thrombin
to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex,
alters the ionic current through the pore. The approach allows the
quantification of nanomolar concentrations of thrombin, and provides
association and dissociation rate constants and equilibrium dissociation
constants for thrombin·aptamer interactions. Aptamer-based nanopores
have the potential to be integrated into arrays for the parallel detection
of multiple analytes.
Collapse
Affiliation(s)
- Dvir Rotem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | | | | | | |
Collapse
|
18
|
Nguyen TH, Pei R, Stojanovic M, Lin Q. Demonstration and Characterization of Biomolecular Enrichment on Microfluidic Aptamer-Functionalized Surfaces. SENSORS AND ACTUATORS. B, CHEMICAL 2011; 155:58-66. [PMID: 21765612 PMCID: PMC3135969 DOI: 10.1016/j.snb.2010.11.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This paper demonstrates and systematically characterizes the enrichment of biomolecular compounds using aptamer-functionalized surfaces within a microfluidic device. The device consists of a microchamber packed with aptamer-functionalized microbeads and integrated with a microheater and temperature sensor to enable thermally controlled binding and release of biomolecules by the aptamer. We first present an equilibrium binding-based analytical model to understand the enrichment process. The characteristics of the aptamer-analyte binding and enrichment are then experimentally studied, using adenosine monophosphate (AMP) and a specific RNA aptamer as a model system. The temporal process of AMP binding to the aptamer is found to be primarily determined by the aptamer-AMP binding kinetics. The temporal process of aptamer-AMP dissociation at varying temperatures is also obtained and observed to occur relatively rapidly (< 2 s). The specificity of the enrichment is next confirmed by performing selective enrichment of AMP from a sample containing biomolecular impurities. Finally, we investigate the enrichment of AMP by either discrete or continuous introduction of a dilute sample into the microchamber, demonstrating enrichment factors ranging from 566 to 686×, which agree with predictions of the analytical model.
Collapse
Affiliation(s)
- Thai Huu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| | - Renjun Pei
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032
| | - Milan Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| |
Collapse
|
19
|
Jing M, Bowser MT. Methods for measuring aptamer-protein equilibria: a review. Anal Chim Acta 2011; 686:9-18. [PMID: 21237304 PMCID: PMC3026478 DOI: 10.1016/j.aca.2010.10.032] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 12/11/2022]
Abstract
Aptamers are single stranded DNA or RNA molecules that have been selected using in vitro techniques to bind target molecules with high affinity and selectivity, rivaling antibodies in many ways. In order to use aptamers in research and clinical applications, a thorough understanding of aptamer-target binding is necessary. In this article, we review methods for assessing aptamer-protein binding using separation based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis, and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry. For each method the principle, range of application and important features, such as sample consumption, experimental time and complexity, are summarized and compared.
Collapse
Affiliation(s)
- Meng Jing
- University of Minnesota, Department of Chemistry, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
| | | |
Collapse
|
20
|
Wang J, Zhang Y, Okamoto Y, Kaji N, Tokeshi M, Baba Y. Online transient isotachophoresis concentration by the pseudo-terminating electrolyte buffer for the separation of DNA-aptamer and its thrombin complex in poly(methyl methacrylate) microchip. Analyst 2011; 136:1142-7. [PMID: 21270992 DOI: 10.1039/c0an00434k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Online automatic transient isotachophoresis concentration of DNA-aptamer and its thrombin complex by using one kind of pseudo-terminating electrolyte buffer in a cross-channel poly(methyl methacrylate) microchip is reported. Sample injection, transient concentration and separation were done continuously and controlled by a sequential voltage switching program, time-consuming steps and complicated chip design were not required. Peak resolution between DNA-aptamer and its thrombin complex was influenced by this novel pseudo-terminating electrolyte buffer, which was prepared by the addition of chemical component with slow mobility into the same buffer as leading electrolyte buffer. 1100-fold signal enhancement of thrombin complex was achieved by this transient isotachophoresis on a standard cross-form microchip. The concentration effect or standing time of transient isotachophoresis was proved to be influenced by the concentration of leading electrolyte ion and the concentration of pseudo-terminating electrolyte buffer ion (glycine). The transient concentration was followed by on-chip nondenaturing gel electrophoresis in methylcellulose solution for the size-based separation. The detection limit, taken as the lowest thrombin concentration at threefold S/N, was determined to be 0.5 amol in mass by this method.
Collapse
Affiliation(s)
- Jun Wang
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
| | | | | | | | | | | |
Collapse
|
21
|
Xu Y, Yang X, Wang E. Review: Aptamers in microfluidic chips. Anal Chim Acta 2010; 683:12-20. [PMID: 21094377 DOI: 10.1016/j.aca.2010.10.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 09/13/2010] [Accepted: 10/03/2010] [Indexed: 01/07/2023]
Abstract
This review, covering reports published from 2002 to August 2010, shows how aptamers have made significant contributions in the improvements of microfluidic chips for affinity extraction, separations and detections. Furthermore, microfluidic chip methods for studying aptamer-target interactions and performing aptamer selections have also been summarized. Accordingly, research vacancies and future development trends in these areas are discussed.
Collapse
Affiliation(s)
- Yuanhong Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | | | | |
Collapse
|
22
|
Kanu AB, Hampikian G, Brandt SD, Hill HH. Ribonucleotide and ribonucleoside determination by ambient pressure ion mobility spectrometry. Anal Chim Acta 2010; 658:91-7. [PMID: 20082780 PMCID: PMC2898576 DOI: 10.1016/j.aca.2009.10.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/13/2009] [Accepted: 10/26/2009] [Indexed: 11/27/2022]
Abstract
Detection limits and reduced mobilities for 12 ribonucleotides and 4 ribonucleosides were measured by ambient pressure electrospray ionization-ion mobility spectrometry (ESI-IMS). With the instrument used in this study it was possible to separate some of these compounds within mixtures. Detection limits reported for ribonucleotides and ribonucleosides ranged from 15 to 300 pmol and the reduced mobilities ranged from 41 to 56 suggesting that ambient pressure ESI-IMS may be used for their rapid and sensitive separation and detection. This report demonstrates that it was possible to use ion mobility spectrometry (IMS) to obtain a spectrum for the separation of nucleotides and nucleosides in less than 1 min. The application holds great promise for nucleotide analysis in the area of separating DNA fragments in genome sequencing and also for forensics DNA typing examinations used for the identification of blood stains in crime scenes and paternity testing.
Collapse
Affiliation(s)
- Abu B Kanu
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA.
| | | | | | | |
Collapse
|
23
|
|
24
|
Krawczyk T, Kondo M, Azam MG, Zhang H, Shibata T, Kai M. Alginic acid-based macromolecular chemiluminescent probe for universal protein assay on a solid-phase membrane. Analyst 2010; 135:2894-900. [DOI: 10.1039/c0an00282h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
25
|
|
26
|
Anderot M, Nilsson M, Végvári Á, Moeller EH, van de Weert M, Isaksson R. Determination of dissociation constants between polyelectrolytes and proteins by affinity capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:892-6. [DOI: 10.1016/j.jchromb.2009.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 02/05/2009] [Accepted: 02/06/2009] [Indexed: 11/28/2022]
|
27
|
Song M, Zhang Y, Li T, Wang Z, Yin J, Wang H. Highly sensitive detection of human thrombin in serum by affinity capillary electrophoresis/laser-induced fluorescence polarization using aptamers as probes. J Chromatogr A 2008; 1216:873-8. [PMID: 19095238 DOI: 10.1016/j.chroma.2008.11.085] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 11/25/2008] [Accepted: 11/27/2008] [Indexed: 11/19/2022]
Abstract
The detection and quantification of disease-related proteins play critical roles in clinical practice and diagnostic assays. We present an affinity probe capillary electrophoresis/laser-induced fluorescence polarization (APCE/LIFP) assay for detection of human thrombin using a specific aptamer as probe. In the APCE/LIFP assay, the mobility and fluorescence polarization of complex are measured simultaneously during CE analysis. The affinity complex of human thrombin can be well separated from unbound aptamer on CE and clearly identified on the basis of its fluorescence polarization and migration. Because of the binding favorable G-quartet conformation potentially involved in the specific aptamer, it was assumed that monovalent and bivalent cations promoting the formation of a stable G quadruplex conformation in the aptamer may enhance the binding of the aptamer and thrombin. Therefore, we investigated the effects of various metal cations on the binding of human thrombin and the aptamer. Our results show that cations like K(+) and Mg(2+) could not stabilize the affinity complex. Without the use of typical cations, a highly sensitive assay of human thrombin was developed with the corresponding detection limits of 4.38x10(-19) and 2.94x10(-19)mol in mass for standard solution and human serum, respectively.
Collapse
Affiliation(s)
- Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | | | | | | | | | | |
Collapse
|