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Kasahara Y, Irisawa Y, Ozaki H, Obika S, Kuwahara M. 2',4'-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorg Med Chem Lett 2013; 23:1288-92. [PMID: 23374873 DOI: 10.1016/j.bmcl.2012.12.093] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 12/25/2012] [Accepted: 12/28/2012] [Indexed: 01/24/2023]
Abstract
DNA-based aptamers that contain 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) over the entire length were successfully obtained using a capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX) method. A modified DNA library was prepared with an enzyme mix of KOD Dash and KOD mutant DNA polymerases. Forty 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers were isolated from an enriched pool and classified into six groups according to their sequence. 2',4'-BNA/LNA aptamers of groups V and VI bound human thrombin with K(d) values in the range of several 10 nanomolar levels.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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Advances in aptamer screening and small molecule aptasensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:29-67. [PMID: 23851587 DOI: 10.1007/10_2013_225] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
It has been 20 years since aptamer and SELEX (systematic evolution of ligands by exponential enrichment) were described independently by Andrew Ellington and Larry Gold. Based on the great advantages of aptamers, there have been numerous isolated aptamers for various targets that have actively been applied as therapeutic and analytical tools. Over 2,000 papers related to aptamers or SELEX have been published, attesting to their wide usefulness and the applicability of aptamers. SELEX methods have been modified or re-created over the years to enable aptamer isolation with higher affinity and selectivity in more labor- and time-efficient manners, including automation. Initially, most of the studies about aptamers have focused on the protein targets, which have physiological functions in the body, and their applications as therapeutic agents or receptors for diagnostics. However, aptamers for small molecules such as organic or inorganic compounds, drugs, antibiotics, or metabolites have not been studied sufficiently, despite the ever-increasing need for rapid and simple analytical methods for various chemical targets in the fields of medical diagnostics, environmental monitoring, food safety, and national defense against targets including chemical warfare. This review focuses on not only recent advances in aptamer screening methods but also its analytical application for small molecules.
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Abstract
In this research, we used the non-SELEX method to successfully select an aptamer that binds to the protein target (bovine catalase) with a K(D) value in the low micro molar range. The time window was determined for the target and aptamer library by optimizing the buffer conditions using 3 × Tris-glycine-potassium phosphate (TGK) buffer as the run buffer and 1× TGK as the selection buffer to give the biggest complex peak. Fractions were collected by multistep nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM)-based partitioning for three rounds of selection. The fractions from each round were enriched using PCR and the progress of selection was monitored using bulk affinity analysis. Fraction 2 was determined to have the optimal bulk affinity (0.75 μM) and this enriched library was cloned and sequenced giving four aptamer sequences. These sequences were verified using affinity capillary electrophoresis (CAT 1 0.237 μM) and fluorescence intensity measurements (CAT 1 0.430 μM). The specificity of the aptamer was also determined by fluorescence intensity measurements. The results showed that the aptamer with the highest binding affinity showed at least a 100-fold decrease in affinity toward four other proteins (i.e. lysozyme, trypsinogen, chymotrypsinogen A, and myoglobin) tested and this confirmed that the aptamer exhibited a distinct specificity toward bovine catalase. This aptamer will be useful in biosensing, Western blot, and biomarker identification.
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Affiliation(s)
- Jon Ashley
- Department of Chemistry, National University of Singapore, Singapore
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Saxton MJ. Wanted: a positive control for anomalous subdiffusion. Biophys J 2012; 103:2411-22. [PMID: 23260043 DOI: 10.1016/j.bpj.2012.10.038] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/23/2012] [Accepted: 10/10/2012] [Indexed: 11/25/2022] Open
Abstract
Anomalous subdiffusion in cells and model systems is an active area of research. The main questions are whether diffusion is anomalous or normal, and if it is anomalous, its mechanism. The subject is controversial, especially the hypothesis that crowding causes anomalous subdiffusion. Anomalous subdiffusion measurements would be strengthened by an experimental standard, particularly one able to cross-calibrate the different types of measurements. Criteria for a calibration standard are proposed. First, diffusion must be anomalous over the length and timescales of the different measurements. The length-scale is fundamental; the time scale can be adjusted through the viscosity of the medium. Second, the standard must be theoretically well understood, with a known anomalous subdiffusion exponent, ideally readily tunable. Third, the standard must be simple, reproducible, and independently characterizable (by, for example, electron microscopy for nanostructures). Candidate experimental standards are evaluated, including obstructed lipid bilayers; aqueous systems obstructed by nanopillars; a continuum percolation system in which a prescribed fraction of randomly chosen obstacles in a regular array is ablated; single-file diffusion in pores; transient anomalous subdiffusion due to binding of particles in arrays such as transcription factors in randomized DNA arrays; and computer-generated physical trajectories.
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Affiliation(s)
- Michael J Saxton
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California, USA.
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Sundaram P, Kurniawan H, Byrne ME, Wower J. Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci 2012; 48:259-71. [PMID: 23142634 DOI: 10.1016/j.ejps.2012.10.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/27/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
RNA aptamers can fold into complex structures and bind with high affinity and selectivity to various macromolecules, viruses, and cells. They are isolated from a large pool of nucleic acids by a conceptually straightforward iterative selection process called SELEX. Aptamers have enormous potential as therapeutics due to their ability to bind to proteins and specifically inhibit their functions with minimal or no harmful side-effects. The first aptamer therapeutic was FDA approved in 2005 and a number of novel aptamer-based therapeutics are currently undergoing clinical trials for treating diseases such as macular degeneration, choroidal neovascularization, intravascular thrombus, acute coronary syndrome, von Willebrand factor related disorders, von Hippel-Lindau syndrome (VHL), angiomas, acute myeloid leukemia, renal cell carcinoma, non-small cell lung cancer, thrombotic thrombocytopenic purpura, and several others. In this review, we present aptamers in on-going, completed, and terminated clinical studies highlighting their mechanism of action as well as the inherent challenges of aptamer production and use.
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Affiliation(s)
- Padma Sundaram
- Biomimetic & Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 283] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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58
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Deng QP, Tie C, Zhou YL, Zhang XX. Cocaine detection by structure-switch aptamer-based capillary zone electrophoresis. Electrophoresis 2012; 33:1465-70. [PMID: 22648816 DOI: 10.1002/elps.201100680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Aptamers, which are nucleic acid oligonucleotides that can bind targets with high affinity and specificity, have been widely applied as affinity probes in capillary electrophoresis (CE). Due to relative weak interaction between aptamers and small molecules, the application of aptamer-based CE is still limited in certain compounds. A new strategy that is based on the aptamer structure-switch concept was designed for small molecule detection by a novel CE method. A carboxyfluorescein (fluorescein amidite, FAM) label DNA aptamer was first incubated with partial complementary strand (CS), and then the free aptamer and the aptamer-CS duplex were well separated and determined by metal cation mediated CE/laser-induced fluorescence. When the target was introduced into the incubated sample, the hybridized form was destabilized, resulting in the changes of the fluorescence intensities of the free aptamer and the aptamer-CS duplex. The length of CS was investigated and 12 mer CS showed the best sensitivity for the detection of cocaine. The presented CE-LIF method, which combines the separation power of CE with the specificity of interactions occurring between target, aptamer, and CS, could be a universal detection strategy for other aptamer-specified small molecules.
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Affiliation(s)
- Qin-Pei Deng
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry, Peking University, Beijing, China
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Zhu C, Liu J, Ling Y, Yang H, Liu Z, Zheng R, Qin L, Hu Z. Evaluation of the clinical value of ELISA based on MPT64 antibody aptamer for serological diagnosis of pulmonary tuberculosis. BMC Infect Dis 2012; 12:96. [PMID: 22520654 PMCID: PMC3410803 DOI: 10.1186/1471-2334-12-96] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 04/20/2012] [Indexed: 12/16/2022] Open
Abstract
Background Presently, tuberculosis (TB) poses a global threat to human health. The development of reliable laboratory tools is vital to the diagnosis and treatment of TB. MPT64, a protein secreted by Mycobacterium tuberculosis complex, is highly specific for TB, making antibody to MPT64 a reagent specific for the diagnosis of TB. Method Antibody to MPT64 was obtained by a combination of genetic engineering and immunization by the system evolution of ligands by exponential enrichment. A high-affinity aptamer of antibody to MPT64 was selected from a random single-stranded DNA library, and a sandwich ELISA method based on this aptamer was developed. This ELISA method was used to detect TB in 328 serum samples, 160 from patients with pulmonary TB (PTB) and 168 from non-tuberculous controls. Results The minimum limit of detection of the ELISA method was 2.5 mg/L, and its linear range varied from 10 mg/L to 800 mg/L. Its sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and area under the curve, with 95 % confidence intervals, were 64.4 % (56.7 %–71.4 %), 99.4 % (96.7 %–99.9 %), 108.2 (15.3–765.9), 0.350 (0.291–0.442) and 0.819 (0.770–0.868), respectively. No significant difference in sensitivity was observed between sputum smear positive (73/112, 65.2 %) and negative (30/48, 62.5 %) individuals. Conclusions This sandwich ELISA based on an MPT64 antibody aptamer may be useful for the serological diagnosis of PTB, both in sputum smear positive and negative patients.
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Affiliation(s)
- Changtai Zhu
- Department of Medical Laboratory, Changzhou Tumor Hospital Soochow University, Changzhou 213001, China
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60
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WANG YX, YE ZZ, SI CY, YING YB. Application of Aptamer Based Biosensors for Detection of Pathogenic Microorganisms. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [PMCID: PMC7148936 DOI: 10.1016/s1872-2040(11)60542-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aptamer is a kind of synthetic oligonucleotides discriminated by in vitro screening and systematic evolution of exponential enrichment technology (SELEX), which can bind to certain targets (small molecules, proteins, or even entire cells) with extremely high specificity. Owing to the advantages of simple preparation, easy modification and good stability, aptamers have been used to construct biosensors for the detection of pathogenic microorganisms. This paper presents the latest advances in SELEX for screening aptamers for pathogenic microorganisms, demonstrates some reported aptamers for pathogenic microorganisms (protozoa, viruses, bacteria), and reviews aptamer based biosensors for detection of pathogenic microorganisms. Finally, the new trends in aptamer based biosensors for detection of pathogenic microorganisms are also discussed.
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61
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Zhu Y, Chandra P, Ban C, Shim YB. Electrochemical Evaluation of Binding Affinity for Aptamer Selection Using the Microarray Chip. ELECTROANAL 2012. [DOI: 10.1002/elan.201100734] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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62
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63
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Harnessing aptamers for electrochemical detection of endotoxin. Anal Biochem 2012; 424:12-20. [PMID: 22370280 DOI: 10.1016/j.ab.2012.02.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/22/2022]
Abstract
Lipopolysaccharide (LPS), also known as endotoxin, triggers a fatal septic shock; therefore, fast and accurate detection of LPS from a complex milieu is of primary importance. Several LPS affinity binders have been reported so far but few of them have proved their efficacy in developing electrochemical sensors capable of selectively detecting LPS from crude biological liquors. In this study, we identified 10 different single-stranded DNA aptamers showing specific affinity to LPS with dissociation constants (K(d)) in the nanomolar range using a NECEEM-based non-SELEX method. Based on the sequence and secondary structure analysis of the LPS binding aptamers, an aptamer exhibiting the highest affinity to LPS (i.e., B2) was selected to construct an impedance biosensor on a gold surface. The developed electrochemical aptasensor showed excellent sensitivity and specificity in the linear detection range from 0.01 to 1 ng/mL of LPS with significantly reduced detection time compared with the traditional Limulus amoebocyte lysate (LAL) assay.
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64
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Yin BC, Ye BC, Wang H, Zhu Z, Tan W. Colorimetric logic gates based on aptamer-crosslinked hydrogels. Chem Commun (Camb) 2011; 48:1248-50. [PMID: 22158758 DOI: 10.1039/c1cc15639j] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a novel molecular logic gate system based on the incorporation of aptamer-crosslinked hydrogels. Modified gold nanoparticles are used as the output signal, which is visible to the naked eye. This system is designed for AND and OR operations using two chemicals as stimulus inputs.
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Affiliation(s)
- Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, P.R. China
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65
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Advances in binder identification and characterisation: the case of oligonucleotide aptamers. N Biotechnol 2011; 29:550-4. [PMID: 22178698 DOI: 10.1016/j.nbt.2011.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 02/07/2023]
Abstract
Aptamers represent an important class of synthetic protein binders useful for proteome-wide applications. The identification and characterisation of such molecules have been greatly facilitated by the development of Systematic Evolution of Ligands by Exponential Amplification (SELEX). Since then numerous advances and alternatives to improve efficient aptamer discovery have been reported. In the present manuscript we discuss the recent advances performed around the SELEX approach that may help to expand the availability of new aptamers and the subsequent applications that may be developed.
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66
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Zhu G, Lübbecke M, Walter JG, Stahl F, Scheper T. Characterization of Optimal Aptamer-Microarray Binding Chemistry and Spacer Design. Chem Eng Technol 2011. [DOI: 10.1002/ceat.201000551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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67
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Wilson R. Preparation of single-stranded DNA from PCR products with streptavidin magnetic beads. Nucleic Acid Ther 2011; 21:437-40. [PMID: 22047177 DOI: 10.1089/nat.2011.0322] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The preparation of single-stranded DNA from double-stranded PCR products is an essential step in the identification of aptamers by Systematic Evolution of Ligands by EXponential enrichment (SELEX). The most widely used method for producing single-stranded DNA is alkaline denaturation of biotinylated PCR products attached to streptavidin-coated magnetic beads. Recently, it has been suggested that this method may be unsuitable due to the release of interfering amounts of streptavidin and biotinylated DNA. In this article, the alkaline method is compared with a thermal method that is known to release significant amounts of streptavidin and biotinylated DNA. Results show that trace amounts of streptavidin and biotinylated DNA are released in the alkaline method, but this can be curtailed by preconditioning the beads in aqueous sodium hydroxide. The main product in the alkaline method is single-stranded DNA, which is produced in high yield.
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Affiliation(s)
- Robert Wilson
- Institute Of Integrative Biology, Liverpool University, Liverpool, UK.
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68
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Krylova SM, Dove PM, Kanoatov M, Krylov SN. Slow-dissociation and slow-recombination assumptions in nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem 2011; 83:7582-5. [PMID: 21853979 DOI: 10.1021/ac2018876] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic affinity method with both analytical and preparative applications. NECEEM requires that the dissociation of the complexes be negligible in its first phase and the recombination of the dissociated complexes be negligible in its second phase. Here, we introduce a method, which facilitates easy examination of whether or not these requirements are satisfied. We derived expressions for two parameters, termed the slow-dissociation parameter (SDP) and slow-recombination parameter (SRP), which can be used to assess the assumptions. Both parameters should be much less than 1 for the assumptions to be satisfied. We calculated the two parameters for new and previously published NECEEM experiments and found that the assumptions were satisfied in all of them. Finally, we discuss changes to NECEEM conditions that should be done if the assumptions are found not to be satisfied. The SDP/SRP assessment helps to easily validate the results of NECEEM-based analyses and thus makes the NECEEM method more robust.
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Affiliation(s)
- Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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69
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de Jong S, Krylov SN. Protein labeling enhances aptamer selection by methods of kinetic capillary electrophoresis. Anal Chem 2011; 83:6330-5. [PMID: 21728308 DOI: 10.1021/ac201242r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate highly efficient selection of DNA aptamers for protein targets. The inability to detect native proteins at low concentrations in capillary electrophoresis creates, however, a significant obstacle for many important protein targets. Here we suggest that protein labeling with new Chromeo dyes can help to overcome this obstacle. By labeling a number of proteins with Chromeo P503, we show that the labeling procedure enables accurate detection of proteins in CE without significantly affecting their electrophoretic mobility or their ability to bind DNA. Moreover, Chromeo P503 does not appear to label the amino-groups of buffer components to a significant extent, making the labeling procedure compatible with a large number of selection and run buffers. Fluorescent labeling of protein targets with Chromeo dyes empowers selection of aptamers by KCE methods and promises to increase the rate at which aptamers for new targets are being developed and introduced in various applications.
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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.
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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
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Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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72
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Carrasco-Correa EJ, Beneito-Cambra M, Herrero-Martínez JM, Ramis-Ramos G. Evaluation of molecular mass and tacticity of polyvinyl alcohol by non-equilibrium capillary electrophoresis of equilibrium mixtures of a polymer and a dye. J Chromatogr A 2011; 1218:2334-41. [DOI: 10.1016/j.chroma.2011.02.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 10/18/2022]
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73
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Mironov GG, Okhonin V, Gorelsky SI, Berezovski MV. Revealing Equilibrium and Rate Constants of Weak and Fast Noncovalent Interactions. Anal Chem 2011; 83:2364-70. [DOI: 10.1021/ac200010u] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Gleb G. Mironov
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
| | - Victor Okhonin
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
| | - Serge I. Gorelsky
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie Curie, Ottawa, Canada K1N 6N5
| | - Maxim V. Berezovski
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
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74
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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.
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Affiliation(s)
- Meng Jing
- University of Minnesota, Department of Chemistry, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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Abstract
Nucleic acid aptamers are in vitro-selected small, single-stranded DNA or RNA oligonucleotides that can specifically recognize their target on the basis of their unique 3-dimensional structures. Recent advances in the development of escort aptamers to deliver and enhance the efficacy of other therapeutic agents have drawn enthusiasm in exploiting cell-type-specific aptamers as drug delivery vehicles. This review mainly focuses on the recent developments of aptamer-mediated targeted delivery systems. We also place particular emphasis on aptamers evolved against cell membrane receptors and possibilities for translation to clinical applications.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, USA
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76
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Turner DJ, Tuytten R, Janssen KP, Lammertyn J, Wuyts J, Pollet J, Eyckerman S, Brown C, Kas K. Toward Clinical Proteomics on a Next-Generation Sequencing Platform. Anal Chem 2010; 83:666-70. [DOI: 10.1021/ac102666n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel J. Turner
- Sequencing Technology Development, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Robin Tuytten
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Kris P.F. Janssen
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Jeroen Lammertyn
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Jan Wuyts
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Jeroen Pollet
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Sven Eyckerman
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Clive Brown
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Koen Kas
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
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77
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Tok J, Lai J, Leung T, Li SFY. Selection of aptamers for signal transduction proteins by capillary electrophoresis. Electrophoresis 2010; 31:2055-62. [PMID: 20564698 DOI: 10.1002/elps.200900543] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
High-affinity aptamers for important signal transduction proteins, i.e. Cdc42-GTP, p21-activated kinase1 (PAK1) and MRCK (myotonic dystrophy kinase-related Cdc42-binding kinase) alpha were successfully selected in the low micro- to nanomolar range using non-systematic evolution of ligands by exponential enrichment (SELEX) with at least three orders of magnitude enhancement from their respective bulk affinity of naïve DNA library. In the non-SELEX procedure, CE was used as a highly efficient affinity method to select aptamers for the desired molecular target through a process that involved repetitive steps of partitioning, known as non-equilibrium CE of equilibrium mixtures with no PCR amplification between successive steps. Various non-SELEX conditions including the type, concentration and pH of the run buffer were optimized. Other considerations such as salt composition of selection buffer, protein concentration and sample injection size were also studied for high stringency during selection. After identifying the best enriched aptamer pool, randomly selected clones from the aptamer pool were sequenced to obtain the individual DNA sequences. The dissociation constants (K(d)) of these sequences were in the low micromolar to nanomolar range, indicating high affinity to the respective proteins. The best binders were also subjected to sequence alignment to generate a phylogenetic tree. No significant consensus region based on approximately 50 sequences for each protein was observed, suggesting the high efficiency of non-SELEX for the selection of numerous unique sequences with high selectivity.
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Affiliation(s)
- Junie Tok
- Department of Chemistry, National University of Singapore, Republic of Singapore, Singapore
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78
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Musheev MU, Filiptsev Y, Okhonin V, Krylov SN. Electric Field Destabilizes Noncovalent Protein−DNA Complexes. J Am Chem Soc 2010; 132:13639-41. [DOI: 10.1021/ja105754h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael U. Musheev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Yuri Filiptsev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Victor Okhonin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
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79
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Kasahara Y, Kitadume S, Morihiro K, Kuwahara M, Ozaki H, Sawai H, Imanishi T, Obika S. Effect of 3'-end capping of aptamer with various 2',4'-bridged nucleotides: Enzymatic post-modification toward a practical use of polyclonal aptamers. Bioorg Med Chem Lett 2010; 20:1626-9. [PMID: 20153191 DOI: 10.1016/j.bmcl.2010.01.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 12/18/2009] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
Abstract
The capping of the 3'-ends of thrombin binding aptamers (TBAs) with bridged nucleotides increased the nuclease resistances and the stabilities in human serum. The binding abilities of the aptamers were not affected by the capping. The capping could be simply executed via a one step enzymatic process using 2',4'-bridged nucleoside 5'-triphosphate and terminal deoxynucleotidyl transferase.
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Affiliation(s)
- Yuuya Kasahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Gunma 376-8515, Japan
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80
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Meng J, Zhang W, Cao CX, Fan LY, Wu J, Wang QL. Moving affinity boundary electrophoresis and its selective isolation of histidine in urine. Analyst 2010; 135:1592-9. [DOI: 10.1039/c000472c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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81
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Affiliation(s)
- Michael Famulok
- LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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82
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Beneito-Cambra M, Herrero-Martínez J, Ramis-Ramos G. Characterization and determination of poly(vinylpyrrolidone) by complexation with an anionic azo-dye and nonequilibrium capillary electrophoresis. J Chromatogr A 2009; 1216:9014-21. [DOI: 10.1016/j.chroma.2009.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Revised: 10/23/2009] [Accepted: 11/02/2009] [Indexed: 11/28/2022]
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83
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Goulko AA, Li F, Chris Le X. Bioanalytical applications of aptamer and molecular-beacon probes in fluorescence-affinity assays. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2009.03.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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84
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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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85
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Potty ASR, Kourentzi K, Fang H, Jackson GW, Zhang X, Legge GB, Willson RC. Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor. Biopolymers 2009; 91:145-56. [PMID: 19025993 DOI: 10.1002/bip.21097] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The binding of a DNA aptamer (5'-CCGTCTTCCAGACAAGAGTGCAGGG-3') to recombinant human vascular endothelial growth factor (VEGF(165)) was characterized using surface plasmon resonance (SPR), fluorescence anisotropy and isothermal titration calorimetry (ITC). Results from both fluorescence anisotropy and ITC indicated that a single aptamer molecule binds to each VEGF homodimer, unlike other VEGF inhibitors that exhibit 2(ligand):1(VEGF homodimer) stoichiometry. In addition, ITC revealed that the association of the aptamer to VEGF at 20 degrees C is enthalpically driven, with an unfavorable entropy contribution. SPR kinetic studies, with careful control of possible mass transfer effects, demonstrated that the aptamer binds to VEGF with an association rate constant k(on) = 4.79 +/- 0.03 x 10(4) M(-1) s(-1) and a dissociation rate constant k(off) = 5.21 +/- 0.02 x 10(-4) s(-1) at 25 degrees C. Key recognition hot-spots were determined by a combination of aptamer sequence substitutions, truncations, and extensions. Most single-nucleotide substitutions, particularly within an mfold-predicted stem, suppress binding, whereas those within a predicted loop have a minimal effect. The 5'-end of the aptamer plays a key role in VEGF recognition, as a single-nucleotide truncation abolished VEGF binding. Conversely, an 11-fold increase in the association rate (and affinity) is observed with a single cytosine nucleotide extension, due to pairing of the 3'-GGG with 5'-CCC in the extended aptamer. Our approach effectively maps the secondary structural elements in the free aptamer, which present the unpaired interface for high affinity VEGF recognition. These data demonstrate that a directed binding analysis can be used in concert with library screening to characterize and improve aptamer/ligand recognition.
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86
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Drabovich AP, Berezovski MV, Musheev MU, Krylov SN. Selection of smart small-molecule ligands: the proof of principle. Anal Chem 2009; 81:490-4. [PMID: 19055427 DOI: 10.1021/ac8023813] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of drugs and diagnostics with desirable characteristics requires smart small-molecule ligandsligands with predefined binding parameters of interaction with the target. Here, we propose a general approach for selection of such ligands from highly diverse combinatorial libraries of small molecules by methods of kinetic capillary electrophoresis (KCE). We deduct three fundamental requirements for the combinatorial library to suit the KCE-based selection of smart ligands and suggest a universal design of the library for selecting smart small-molecule ligands: every small molecule in the library is tagged with DNA that encodes the structure of the molecule. Finally, we use several DNA-tagged small molecules, which represent a hypothetical library, to prove experimentally selection of smart small-molecule ligands by the proposed approach.
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Affiliation(s)
- Andrei P Drabovich
- Department of Chemistry, York University, Toronto, Ontario M3J1P3, Canada
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87
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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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88
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Yunusov D, So M, Shayan S, Okhonin V, Musheev MU, Berezovski MV, Krylov SN. Kinetic capillary electrophoresis-based affinity screening of aptamer clones. Anal Chim Acta 2008; 631:102-7. [PMID: 19046686 DOI: 10.1016/j.aca.2008.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 10/02/2008] [Accepted: 10/07/2008] [Indexed: 02/07/2023]
Abstract
DNA aptamers are single stranded DNA (ssDNA) molecules artificially selected from random-sequence DNA libraries for their specific binding to a certain target. DNA aptamers have a number of advantages over antibodies and promise to replace them in both diagnostic and therapeutic applications. The development of DNA aptamers involves three major stages: library enrichment, obtaining individual DNA clones, and the affinity screening of the clones. The purpose of the screening is to obtain the nucleotide sequences of aptamers and the binding parameters of their interaction with the target. Highly efficient approaches have been recently developed for the first two stages, while the third stage remained the rate-limiting one. Here, we introduce a new method for affinity screening of individual DNA aptamer clones. The proposed method amalgamates: (i) aptamer amplification by asymmetric PCR (PCR with a primer ratio different from unity), (ii) analysis of aptamer-target interaction, combining in-capillary mixing of reactants by transverse diffusion of laminar flow profiles (TDLFP) and affinity analysis using kinetic capillary electrophoresis (KCE), and (iii) sequencing of only aptamers with satisfying binding parameters. For the first time we showed that aptamer clones can be directly used in TDLFP/KCE-based affinity analysis without an additional purification step after asymmetric PCR amplification. We also demonstrated that mathematical modeling of TDLFP-based mixing allows for the determination of K(d) values for the in-capillary reaction of an aptamer and a target and that the obtained K(d) values can be used for the accurate affinity ranking of aptamers. The proposed method does not require the knowledge of aptamer sequences before screening, avoids lengthy (3-5 h) purification steps of aptamer clones, and minimizes reagent consumption to nanoliters.
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Affiliation(s)
- Diana Yunusov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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89
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Musheev MU, Javaherian S, Okhonin V, Krylov SN. Diffusion as a Tool of Measuring Temperature inside a Capillary. Anal Chem 2008; 80:6752-7. [DOI: 10.1021/ac8009406] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael U. Musheev
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sahar Javaherian
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Victor Okhonin
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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90
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Kostal V, Katzenmeyer J, Arriaga EA. Capillary electrophoresis in bioanalysis. Anal Chem 2008; 80:4533-50. [PMID: 18484738 DOI: 10.1021/ac8007384] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vratislav Kostal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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91
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Li XM, Zhang F, Zhang SS. Capillary electrophoresis enzyme immunoassay for alpha-fetoprotein and thyroxine in human serum with electrochemical detection. J Sep Sci 2008; 31:336-40. [DOI: 10.1002/jssc.200700340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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92
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Song EJ, Babar SME, Oh E, Hasan MN, Hong HM, Yoo YS. CE at the omics level: Towards systems biology – An update. Electrophoresis 2008; 29:129-42. [DOI: 10.1002/elps.200700467] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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93
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Abstract
The high affinity and specificity of aptamers make them ideal reagents for a wide range of analytical applications. It is not surprising that they are finding application in microfluidics as well. CE has proven to be an efficient technique for isolating aptamers. Aptamers have been used as affinity reagents in CE assays. Aptamer-based chromatography stationary phases have demonstrated unique selectivities. Possibly the application that holds the highest potential is aptamer microarrays for screening proteomic samples.
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94
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Radko SP, Rakhmetova SY, Bodoev NV, Archakov AI. Aptamers as affinity reagents for clinical proteomics. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2007. [DOI: 10.1134/s1990750807030043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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95
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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96
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Berezovski MV, Musheev MU, Drabovich AP, Jitkova JV, Krylov SN. Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides. Nat Protoc 2007; 1:1359-69. [PMID: 17406423 DOI: 10.1038/nprot.2006.200] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are typically selected from libraries of random DNA (or RNA) sequences through systematic evolution of ligands by exponential enrichment (SELEX), which involves several rounds of alternating steps of partitioning of candidate oligonucleotides and their PCR amplification. Here we describe a protocol for non-SELEX selection of aptamers--a process that involves repetitive steps of partitioning with no amplification between them. Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), which is a highly efficient affinity method, is used for partitioning. NECEEM also facilitates monitoring of bulk affinity of enriched libraries at every step of partitioning and screening of individual clones for their affinity to the target. NECEEM allows all clones to be screened prior to sequencing, so that only clones with suitable binding parameters are sequenced. The entire protocol can be completed in 1 wk, whereas conventional SELEX protocols take several weeks even in a specialized industrial facility.
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Affiliation(s)
- Maxim V Berezovski
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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97
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Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 933] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
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Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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98
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Abstract
Kinetic capillary electrophoresis (KCE) is defined as capillary electrophoresis of species that interact during electrophoresis. KCE can serve as a conceptual platform for development of homogeneous kinetic affinity methods for affinity measurements (measurements of binding parameters and quantitative measurements) and affinity purification (purification of known molecules and search of unknown molecules). A number of different KCE methods can be designed by varying initial and boundary conditions - the way interacting species enter and exit the capillary. KCE methods will find multiple practical applications in the designing of biomedical diagnostics and the development of drug candidates. Here, the concept of KCE, its up-to-date applications, and future prospective are reviewed.
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Affiliation(s)
- Sergey N Krylov
- Department of Chemistry, York University, Toronto, Ontario, Canada.
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