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Liu Y, Le C, Tyrrell DL, Le XC, Li XF. Aptamer Binding Assay for the E Antigen of Hepatitis B Using Modified Aptamers with G-Quadruplex Structures. Anal Chem 2020; 92:6495-6501. [PMID: 32250595 DOI: 10.1021/acs.analchem.9b05740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The e antigen of hepatitis B (HBeAg) is positively associated with an increased risk of developing liver cancer and cirrhosis in chronic hepatitis B (CHB) patients. Clinical monitoring of HBeAg provides guidance to the treatment of CHB and the assessment of disease progression. We describe here an affinity binding assay for HBeAg, which takes advantage of G-quadruplex aptamers for enhanced binding and stability. We demonstrate a strategy to improve the binding affinity of aptamers by modifying their sequences upon their G-quadruplex and secondary structures. On the basis of predicting a stable G-quadruplex and a secondary structure, we truncated 19 nucleotides (nt) from the primer regions of an 80-nt aptamer, and the resulting 61-nt aptamer enhanced binding affinity by 19 times (Kd = 1.2 nM). We mutated a second aptamer (40 nt) in one loop region and incorporated pyrrolo-deoxycytidine to replace deoxycytidine in another loop. The modified 40-nt aptamer, with a stable G-quadruplex and two modified loops, exhibited a 100 times higher binding affinity for HBeAg (Kd = 0.4 nM) than the unmodified original aptamer. Using the two newly modified aptamers, one serving as the capture and the other as the reporter, we have developed an improved sandwich binding assay for HBeAg. Analyses of HBeAg in serum samples (concentration ranging from 0.1 to 60 ng/mL) of 10 hepatitis B patients, showing consistent results with clinical tests, demonstrate a successful application of the aptamer modification strategy and the associated aptamer binding assay.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - D Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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Chawjiraphan W, Apiwat C, Segkhoonthod K, Treerattrakoon K, Pinpradup P, Sathirapongsasuti N, Pongprayoon P, Luksirikul P, Isarankura-Na-Ayudhya P, Japrung D. Sensitive detection of albuminuria by graphene oxide-mediated fluorescence quenching aptasensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:118128. [PMID: 32066078 DOI: 10.1016/j.saa.2020.118128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/12/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Albuminuria is a pathological condition wherein the human serum albumin (HSA) protein is present in abnormally excess amounts in the urine. A simple and sensitive graphene oxide-mediated fluorescence quenching aptasensor is developed to quantify albumin in urine samples and HSA in serum samples. The aptamer-bound HSA used in this aptasensor has hairpin structures, which are characteristic of the aptamer binding site. The limit of detection of the developed platform is 0.05 μg·mL-1 and the detection range is 0.1-14.0 μg·mL-1, which covers the albuminuria concentration range present in normal human urine and the urine of the patient with kidney diseases. This approach can be modified to measure HSA using a high-throughput quantification platform and portable point of care testing. In addition, the production cost for one reaction is cheaper than those for other standard automated methods. Therefore, this aptasensor has significant potential for commercialization and wide-scale public use.
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Affiliation(s)
- Wireeya Chawjiraphan
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand
| | - Chayachon Apiwat
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand; Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Khoonsake Segkhoonthod
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand
| | - Kiatnida Treerattrakoon
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand
| | - Preedee Pinpradup
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand
| | - Nuankanya Sathirapongsasuti
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand; Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Patraporn Luksirikul
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand; Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | | | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani, Thailand.
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53
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Zhao Q, Bai Y, Wang H. Directing a rational design of aptamer-based fluorescence anisotropy assay for sensitive detection of immunoglobulin E by site-specific binding study. Talanta 2020; 217:121018. [PMID: 32498825 DOI: 10.1016/j.talanta.2020.121018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 11/17/2022]
Abstract
Mapping aptamer-protein interactions is important for characterization and applications of aptamers against proteins. We describe here probing affinity interactions between aptamer and immunoglobulin E (IgE) with a fluorescence anisotropy (FA) approach using a series of aptamer probes having single fluorescein (FAM) label at individual nucleotide (A, C, T). Studies of binding between IgE and aptamer probes revealed several possible close-contact sites, e.g., T9, T10, T11, T13, C15, and T17 of a 37-nt aptamer with a stem-loop secondary structure. FAM labeling on these sites resulted in much higher FA values (higher than 0.230 for T10, T11, T13 and C15) of aptamer-IgE complexes than the distant sites (e.g., terminals) of aptamer probably because the bound IgE close to these sites significantly restricted local rotation of FAM. Close-contact site labeled aptamer probes with high affinity allowed to develop a more sensitive FA assay for IgE than distant site labeled aptamers. The FA assay using T10-labeled aptamer with a dissociation constant (Kd) about 0.8 nM enabled selective detection of IgE at 20 pM and large FA increase upon IgE addition. We also found A12, C14, A25, and T27 were important for IgE-aptamer binding as FAM labeling at these sites significantly reduced aptamer affinity. FA study showed the loop region of this stem-loop aptamer was crucial for affinity binding, and IgE bound to the loop. This FA method will be helpful for understanding aptamer-protein binding and making a rational design of aptamer affinity assays for proteins.
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Affiliation(s)
- Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yunlong Bai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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54
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Li N, Shi K, Rao T, Banerjee S, Aihara H. Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase. Sci Rep 2020; 10:393. [PMID: 31941902 PMCID: PMC6962361 DOI: 10.1038/s41598-019-56825-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/17/2019] [Indexed: 01/07/2023] Open
Abstract
Fowlpox virus resolvase (Fpr) is an endonuclease that cleaves a broad range of branched DNA structures, including the Holliday junction (HJ), with little sequence-specificity. To better understand the mechanisms underlying its relaxed substrate specificity, we determined the crystal structures of Fpr and that in a novel complex with HJ at 3.1-Å resolution. In the Fpr-HJ complex, two Fpr dimers use several distinct regions to interact with different DNA structural motifs, showing versatility in DNA-binding. Biochemical and solution NMR data support the existence of non-canonical modes of HJ interaction in solution. The binding of Fpr to various DNA motifs are mediated by its flat DNA-binding surface, which is centered on a short loop spanning K61 to I72 and flanked by longer α-helices at the outer edges, and basic side grooves near the dimer interface. Replacing the Fpr loop K61~I72 with a longer loop from Thermus thermophilus RuvC (E71~A87) endows Fpr with an enhanced selectivity toward HJ cleavage but with a target sequence preference distinct from that of RuvC, highlighting a unique role of this loop region in Fpr-HJ interaction. Our work helps explain the broad substrate selectivity of Fpr and suggests a possible mode of its association with poxvirus hairpin telomeres.
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Affiliation(s)
- Na Li
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA ,0000 0001 0703 7066grid.412099.7Present Address: College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001 People’s Republic of China
| | - Ke Shi
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
| | - Timsi Rao
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
| | - Surajit Banerjee
- 0000 0001 1939 4845grid.187073.aNortheastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois 60439 USA
| | - Hideki Aihara
- 0000000419368657grid.17635.36Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, Minneapolis, MN 55455 USA
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55
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Wan Y, Zhao J, He J, Lou X. Nano-Affi: a solution-phase, label-free, colorimetric aptamer affinity assay based on binding-inhibited aggregation of gold nanoparticles. Analyst 2020; 145:4276-4282. [DOI: 10.1039/d0an00827c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ideal way to assess aptamer affinity is when both aptamer and target are in a native state, without the unpredictable interference associated with labelling and surface immobilization.
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Affiliation(s)
- Yuan Wan
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Jiaxing Zhao
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing
- China
| | - Xinhui Lou
- Department of Chemistry
- Capital Normal University
- Beijing
- China
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56
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Kinetic and Thermodynamic Analyses of RNA-Protein Interactions. Methods Mol Biol 2020. [PMID: 31889255 DOI: 10.1007/978-1-0716-0231-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recently created biophysical methods, such as surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC), have been widely used to quantitatively study biomolecule interactions. The dissociation constant of the interaction with kinetic parameters, such as association rate constant and dissociation rate constant, can be obtained using SPR analysis. With thermodynamic parameters, such as enthalpy change and entropy change, the dissociation constant can be obtained by ITC analysis. Both methods differ not only in the type of information obtained but also in throughput and sample concentration. Analyzing the biophysical parameters of RNA-protein interactions will help us understand their functions in biological processes. In this chapter, we describe step-by-step SPR and ITC protocols suitable to study the kinetics and thermodynamics of RNA-protein interactions.
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57
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Kim K, Lee CH, Park CB. Chemical sensing platforms for detecting trace-level Alzheimer's core biomarkers. Chem Soc Rev 2020; 49:5446-5472. [DOI: 10.1039/d0cs00107d] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This review provides an overview of recent advances in optical and electrical detection of Alzheimer's disease biomarkers in clinically relevant fluids.
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Affiliation(s)
- Kayoung Kim
- Department of Materials Science and Engineering
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
| | - Chang Heon Lee
- Department of Materials Science and Engineering
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
| | - Chan Beum Park
- Department of Materials Science and Engineering
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
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58
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Aptamer-Based Nanoporous Anodic Alumina Interferometric Biosensor for Real-Time Thrombin Detection. SENSORS 2019; 19:s19204543. [PMID: 31635027 PMCID: PMC6833485 DOI: 10.3390/s19204543] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/18/2022]
Abstract
Aptamer biosensors are one of the most powerful techniques in biosensing. Achieving the best platform to use in aptamer biosensors typically includes crucial chemical modifications that enable aptamer immobilization on the surface in the most efficient manner. These chemical modifications must be well defined. In this work we propose nanoporous anodic alumina (NAA) chemically modified with streptavidin as a platform for aptamer immobilization. The immobilization of biotinylated thrombin binding aptamer (TBA) was monitored in real time by means of reflective interferometric spectroscopy (RIfS). The study has permitted to characterize in real time the path to immobilize TBA on the inner pore walls of NAA. Furthermore, this study provides an accurate label-free method to detect thrombin in real-time with high affinity and specificity.
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59
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Ahmad AA, Kasim KF, Ma’Radzi AH, Gopinath SC. Peptic ulcer: Current prospects of diagnostic and nanobiotechnological trends on pathogenicity. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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60
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Sass S, Stöcklein WFM, Klevesath A, Hurpin J, Menger M, Hille C. Binding affinity data of DNA aptamers for therapeutic anthracyclines from microscale thermophoresis and surface plasmon resonance spectroscopy. Analyst 2019; 144:6064-6073. [PMID: 31528891 DOI: 10.1039/c9an01247h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Anthracyclines like daunorubicin (DRN) and doxorubicin (DOX) play an undisputed key role in cancer treatment, but their chronic administration can cause severe side effects. For precise anthracycline analytical systems, aptamers are preferable recognition elements. Here, we describe the detailed characterisation of a single-stranded DNA aptamer DRN-10 and its truncated versions for DOX and DRN detection. Binding affinities were determined from surface plasmon resonance (SPR) and microscale thermophoresis (MST) and combined with conformational data from circular dichroism (CD). Both aptamers displayed similar nanomolar binding affinities to DRN and DOX, even though their rate constants differed as shown by SPR recordings. SPR kinetic data unravelled a two-state reaction model including a 1 : 1 binding and a subsequent conformational change of the binding complex. This model was supported by CD spectra. In addition, the dissociation constants determined with MST were always lower than that from SPR, and especially for the truncated aptamer they differed by two orders of magnitude. This most probably reflects the methodological difference, namely labelling for MST vs. immobilisation for SPR. From CD recordings, we suggested a specific G-quadruplex as structural basis for anthracycline binding. We concluded that the aptamer DRN-10 is a promising recognition element for anthracycline detection systems and further selected aptamers can be also characterised with the combined methodological approach presented here.
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Affiliation(s)
- Stephan Sass
- Physical Chemistry/ALS ComBi, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Walter F M Stöcklein
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalysis and Bioprocesses (IZI-BB), 14476 Potsdam, Germany.
| | - Anja Klevesath
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalysis and Bioprocesses (IZI-BB), 14476 Potsdam, Germany.
| | - Jeanne Hurpin
- Physical Chemistry/ALS ComBi, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Marcus Menger
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalysis and Bioprocesses (IZI-BB), 14476 Potsdam, Germany.
| | - Carsten Hille
- Physical Chemistry/ALS ComBi, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany.,Technical University of Applied Sciences Wildau, 15745 Wildau, Germany.
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61
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Raman Spectroscopy and Aptamers for a Label-Free Approach: Diagnostic and Application Tools. JOURNAL OF HEALTHCARE ENGINEERING 2019; 2019:2815789. [PMID: 31183028 PMCID: PMC6512054 DOI: 10.1155/2019/2815789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 01/04/2023]
Abstract
Raman spectroscopy is a powerful optical technique based on the inelastic scattering of incident light to assess the chemical composition of a sample, including biological ones. Medical diagnostic applications of Raman spectroscopy are constantly increasing to provide biochemical and structural information on several specimens, being not affected by water interference, and potentially avoiding the constraint of additional labelling procedures. New strategies have been recently developed to overcome some Raman limitations related, for instance, to the need to deal with an adequate quantity of the sample to perform a reliable analysis. In this regard, the use of metallic nanoparticles, the optimization of fiber optic probes, and other approaches can actually enhance the signal intensity compared to spontaneous Raman scattering. Moreover, to further increase the potential of this investigation technique, aptamers can be considered as a valuable means, being synthetic, short, single, or double-stranded oligonucleotides (RNAs or DNAs) that fold up into unique 3D structures to specifically bind to selected molecules, even at very low concentrations, and thus allowing an early diagnosis of a possible disease. Due to the paramount relevance of the topic, this review focuses on the main Raman spectroscopy techniques combined with aptamer arrays in the label-free mode, providing an overview on different applications to support healthcare management.
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Thompson BR, Soller KJ, Vetter A, Yang J, Veglia G, Bowser MT, Metzger JM. Cytoplasmic nucleic acid-based XNAs directly enhance live cardiac cell function by a Ca 2+ cycling-independent mechanism via the sarcomere. J Mol Cell Cardiol 2019; 130:1-9. [PMID: 30849419 DOI: 10.1016/j.yjmcc.2019.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/05/2019] [Accepted: 02/27/2019] [Indexed: 11/19/2022]
Abstract
Nucleic acid - protein interactions are critical for regulating gene activation in the nucleus. In the cytoplasm, however, potential nucleic acid-protein functional interactions are less clear. The emergence of a large and expanding number of non-coding RNAs and DNA fragments raises the possibility that the cytoplasmic nucleic acids may interact with cytoplasmic cellular components to directly alter key biological processes within the cell. We now show that both natural and synthetic nucleic acids, collectively XNAs, when introduced to the cytoplasm of live cell cardiac myocytes, markedly enhance contractile function via a mechanism that is independent of new translation, activation of the TLR-9 pathway or by altered intracellular Ca2+ cycling. Findings show a steep XNA oligo length-dependence, but not sequence dependence or nucleic acid moiety dependence, for cytoplasmic XNAs to hasten myocyte relaxation. XNAs localized to the sarcomere in a striated pattern and bound the cardiac troponin regulatory complex with high affinity in an electrostatic-dependent manner. Mechanistically, XNAs phenocopy PKA-based modified troponin to cause faster relaxation. Collectively, these data support a new role for cytoplasmic nucleic acids in directly modulating live cell cardiac performance and raise the possibility that cytoplasmic nucleic acid - protein interactions may alter functionally relevant pathways in other cell types.
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Affiliation(s)
- Brian R Thompson
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Kailey J Soller
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States of America
| | - Anthony Vetter
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Jing Yang
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States of America
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, United States of America
| | - Michael T Bowser
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States of America
| | - Joseph M Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, United States of America.
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63
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Seo M, Lei L, Egli M. Label-Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein-RNA Complexes. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2019; 76:e70. [PMID: 30461222 PMCID: PMC6391183 DOI: 10.1002/cpnc.70] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The electrophoretic mobility shift assay (EMSA) is a well-established method to detect formation of complexes between proteins and nucleic acids and to determine, among other parameters, equilibrium constants for the interaction. Mixtures of protein and nucleic acid solutions of various ratios are analyzed via polyacrylamide gel electrophoresis (PAGE) under native conditions. In general, protein-nucleic acid complexes will migrate more slowly than the free nucleic acid. From the distributions of the nucleic acid components in the observed bands in individual gel lanes, quantitative parameters such as the dissociation constant (Kd ) of the interaction can be measured. This article describes a simple and rapid EMSA that relies either on precast commercial or handcast polyacrylamide gels and uses unlabeled protein and nucleic acid. Nucleic acids are instead detected with SYBR Gold stain and band intensities established with a standard gel imaging system. We used this protocol specifically to determine Kd values for complexes between the PAZ domain of Argonaute 2 (Ago2) enzyme and native and chemically modified RNA oligonucleotides. EMSA-based equilibrium constants are compared to those determined with isothermal titration calorimetry (ITC). Advantages and limitations of this simple EMSA are discussed by comparing it to other techniques used for determination of equilibrium constants of protein-RNA interactions, and a troubleshooting guide is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Minguk Seo
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
| | - Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
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64
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Abstract
To explore thermofluorimetric analysis (TFA) in detail, we compared two related aptamers. The first, LINN2, is a DNA aptamer previously selected against EGFR recombinant protein. In this work we selected a second aptamer, KM4, against EGFR-overexpressing A549 cells. The two aptamers were derived from the same pool and bind the same target but behave differently in TFA. Our results suggest four overall conclusions about TFA of aptamers: 1. Some aptamers show reduced fluorescence upon target binding suggesting that target-bound aptamer is not always fluorescent. 2. Many aptamers do not obey the intuitive assumptions that aptamer-target interactions stabilize a folded conformation. 3. TFA may be most appropriate for aptamers with significant double-stranded structure. 4. Kinetic effects may be significant and the order of operations in preparing samples should be carefully optimized.
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65
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Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. 4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics. Molecules 2019; 24:E602. [PMID: 30744004 PMCID: PMC6384856 DOI: 10.3390/molecules24030602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/26/2019] [Accepted: 02/05/2019] [Indexed: 11/16/2022] Open
Abstract
Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA⁻protein interactions.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Christina M Eng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jeffrey M Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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66
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Cataldo R, Giotta L, Guascito MR, Alfinito E. Assessing the Quality of in Silico Produced Biomolecules: The Discovery of a New Conformer. J Phys Chem B 2019; 123:1265-1273. [PMID: 30642170 DOI: 10.1021/acs.jpcb.8b11456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The computational procedures for predicting the 3D structure of aptamers interacting with different biological molecules have gained increasing attention in recent years. The information acquired through these methods represents a crucial input for research, especially when relevant crystallographic data are not available. A number of software programs able to perform macromolecular docking are currently accessible, leading to the prediction of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Nevertheless, the scoring protocols employed for ranking the candidate structures do not always produce satisfactory results, making difficult the identification of structures that are most likely to occur in nature. In this paper, we propose a novel procedure to improve the predictive performances of computational scoring protocols, using a maximum likelihood estimate based on topological and electrical properties of interacting biomolecules. The reliability of the new computational approach, enabling the ranking of aptamer-protein configurations produced by an open source docking program, has been assessed by its successful application to a set of antiangiopoietin aptamers, for which experimental data highlighting the sequence-dependent affinity toward the target protein are available. The procedure led to the identification of two main types of aptamer conformers involved in angiopoietin binding. Interestingly, one of these reproduces the arrangement of angiopoietin with its natural target, tyrosine kinase, while the other one is completely unexpected. The possible scenarios related to these results have been discussed. The methodology here described can be used to refine the outcomes of different computational procedures and can be applied to a wide range of biological molecules, thus representing a new tool for guiding the design of bioinspired sensors with enhanced selectivity.
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Affiliation(s)
- R Cataldo
- Department of Mathematics and Physics, "Ennio De Giorgi" , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - L Giotta
- Department of Biological and Environmental Sciences and Technologies , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - M R Guascito
- Department of Biological and Environmental Sciences and Technologies , University of Salento , Via Monteroni , I-73100 Lecce , Italy
| | - E Alfinito
- Department of Innovation Engineering , University of Salento , Via Monteroni , I-73100 Lecce , Italy
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Sulatskaya AI, Sulatsky MI, Antifeeva IA, Kuznetsova IM, Turoverov KK. Structural Analogue of Thioflavin T, DMASEBT, as a Tool for Amyloid Fibrils Study. Anal Chem 2019; 91:3131-3140. [DOI: 10.1021/acs.analchem.8b05737] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- A. I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - M. I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Iu. A. Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - I. M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - K. K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
- Peter the Great St. Petersburg Polytechnic University (SPbPU), St. Petersburg 195251, Russia
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Nasiri Khonsari Y, Sun S. Recent trends in electrochemiluminescence aptasensors and their applications. Chem Commun (Camb) 2018; 53:9042-9054. [PMID: 28759057 DOI: 10.1039/c7cc04300g] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aptamers are single stranded DNA or RNA ligands which can be selected for different targets from proteins to small organic dyes. In the past few years great progress has been accomplished in the development of aptamer based bioanalytical assays with different detection techniques. Among them, electrochemiluminescence (ECL) aptasensors are very promising because they have the advantages of both electrochemical and chemiluminescence biosensors, such as high sensitivity, low background, cost effectiveness, and ease of control. In this review, we summarize the recent efforts to construct novel and improved ECL aptasensors and their application.
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Affiliation(s)
- Yasamin Nasiri Khonsari
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi, District, Dalian 116023, China
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69
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Kaur H. Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj 2018; 1862:2323-2329. [PMID: 30059712 DOI: 10.1016/j.bbagen.2018.07.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND SELEX technique is employed to select aptamers against wide range of targets. The in vitro method of aptamer selection using live cells as the target is referred as cell-SELEX. SCOPE OF THE REVIEW The review provides a comprehensive description on the development of aptamers through various cell-SELEX methods and list of aptamers identified through this method. In addition, it pinpoints the advantages and limitations of the cell-SELEX process and its variants. MAJOR CONCLUSIONS The use of aptamers as therapeutic and diagnostic agents is rapidly evolving, selection techniques such as Cell-SELEX could be beneficial in identifying aptamers when the target is in its native conformation and without prior information of the cognate target, thereby bringing the aptamer development one step closer to the clinic. GENERAL SIGNIFICANCE The information in this review can serve as a database for the design and development of futuristic oligonucleotide based diagnostics and therapeutics work.
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Samokhvalov AV, Safenkova IV, Eremin SA, Zherdev AV, Dzantiev BB. Measurement of (Aptamer–Small Target) KD Using the Competition between Fluorescently Labeled and Unlabeled Targets and the Detection of Fluorescence Anisotropy. Anal Chem 2018; 90:9189-9198. [DOI: 10.1021/acs.analchem.8b01699] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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Tabarzad M, Sharafi Z, Javidi J. Covalent immobilization of coagulation factor VIII on magnetic nanoparticles for aptamer development. J Appl Biomater Funct Mater 2018; 16:161-170. [PMID: 29609491 DOI: 10.1177/2280800018765046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Magnetic nanoparticles (MNPs) are one of the most useful particulate systems in analytical applications such as specific aptamer selection. Proteins are the most noted targets of aptamer selection. Generally, covalently immobilized protein coated MNPs are more stable structures. METHODS In this study, coagulation factor VIII (FVIII) was immobilized on MNPs. A silica coating provided isocyanate functional groups was considered to interact covalently with reactive groups of the protein, resulting in a stable protein immobilization. The reactions was run in dried toluene. At end, these MNPs were applied for affinity determination of a previously selected FVIII specific aptamers. RESULTS Immobilization of 1 mg FVIII (~ 3 nmol) on 5 mg particles was achieved with no significant particle aggregation. Using a fluorescence-based method, affinity measurement resulted in a calculated dissociation constant of 120 ± 5.6 nM for the FVIII-specific aptamer to the FVIII-coated MNPs. CONCLUSION The final product could be a suitable protein-coated solid support for magnetic-based aptamer selection processes.
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Affiliation(s)
- Maryam Tabarzad
- 1 Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Sharafi
- 2 Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jaber Javidi
- 3 Department of Pharmaceutics and Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Wu X, Diao D, Lu Z, Han Y, Xu S, Lou X. Phthalic Acid Ester-Binding DNA Aptamer Selection, Characterization, and Application to an Electrochemical Aptasensor. J Vis Exp 2018. [PMID: 29630049 DOI: 10.3791/56814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phthalic acid esters (PAEs) areone of the major groups of persistent organic pollutants. The group-specific detection of PAEs is highly desired due to the rapid growing of congeners. DNA aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward highly hydrophobic small molecule targets, such as PAEs, is rarely reported. This work describes a bead-based method designed to select group-specific DNA aptamers to PAEs. The amino group functionalized dibutyl phthalate (DBP-NH2) as the anchor target was synthesized and immobilized on the epoxy-activated agarose beads, allowing the display of the phthalic ester group at the surface of the immobilization matrix, and therefore the selection of the group-specific binders. We determined the dissociation constants of the aptamer candidates by quantitative polymerization chain reaction coupled with magnetic separation. The relative affinities and selectivity of the aptamers to other PAEs were determined by the competitive assays, where the aptamer candidates were pre-bounded to the DBP-NH2 attached magnetic beads and released to the supernatant upon incubation with the tested PAEs or other potential interfering substances. The competitive assay was applied because it provided a facile affinity comparison among PAEs that had no functional groups for surface immobilization. Finally, we demonstrated the fabrication of an electrochemical aptasensor and used it for ultrasensitive and selective detection of bis(2-ethylhexyl) phthalate. This protocol provides insights for the aptamer discovery of other hydrophobic small molecules.
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Affiliation(s)
- Xiao Wu
- Department of Chemistry, Capital Normal University
| | - Donglin Diao
- Department of Chemistry, Capital Normal University
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University
| | - Yu Han
- Department of Chemistry, Capital Normal University
| | - Shi Xu
- College of Life Sciences, Capital Normal University
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University;
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Lin ZT, DeMarr V, Bao J, Wu T. Molecularly Imprinted Polymer-Based Biosensors: For the Early, Rapid Detection of Pathogens, Biomarkers, and Toxins in Clinical, Environmental, or Food Samples. IEEE NANOTECHNOLOGY MAGAZINE 2018. [DOI: 10.1109/mnano.2017.2779718] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zuan-Tao Lin
- Biomedical Engineering, University of Houston, Houston, Texas United States
| | - Victoria DeMarr
- Biomedical Engineering, University of Houston, Houston, Texas United States
| | - Jiming Bao
- Electrical and Computer Engineering, University of Houston, Houston, Texas United States
| | - Tianfu Wu
- Biomedical Engineering, University of Houston, Houston, Texas United States
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Jacobs A, Hoover H, Smith E, Clemmer DE, Kim CH, Kao CC. The intrinsically disordered N-terminal arm of the brome mosaic virus coat protein specifically recognizes the RNA motif that directs the initiation of viral RNA replication. Nucleic Acids Res 2018; 46:324-335. [PMID: 29140480 PMCID: PMC5758871 DOI: 10.1093/nar/gkx1087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022] Open
Abstract
In the brome mosaic virus (BMV) virion, the coat protein (CP) selectively contacts the RNA motifs that regulate translation and RNA replication (Hoover et al., 2016. J. Virol. 90, 7748). We hypothesize that the unstructured N-terminal arm (NTA) of the BMV CP can specifically recognize RNA motifs. Using ion mobility spectrometry-mass spectrometry, we demonstrate that peptides containing the NTA of the CP were found to preferentially bind to an RNA hairpin motif that directs the initiation of BMV RNA synthesis. RNA binding causes the peptide to change from heterogeneous structures to a single family of structures. Fluorescence anisotropy, fluorescence quenching and size exclusion chromatography experiments all confirm that the NTA can specific recognize the RNA motif. The peptide introduced into plants along with BMV virion increased accumulation of the BMV CP and accelerated the rate of minus-strand RNA synthesis. The intrinsically disordered BMV NTA could thus specifically recognize BMV RNAs to affect viral infection.
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Affiliation(s)
- Alexander Jacobs
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Haley Hoover
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Edward Smith
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Chul-Hyun Kim
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - C Cheng Kao
- Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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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.
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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
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Ruscito A, McConnell EM, Koudrina A, Velu R, Mattice C, Hunt V, McKeague M, DeRosa MC. In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target. ACTA ACUST UNITED AC 2017; 9:233-268. [PMID: 29241295 DOI: 10.1002/cpch.28] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Erin M McConnell
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Anna Koudrina
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Ranganathan Velu
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | | | - Vernon Hunt
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Maria C DeRosa
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
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Competitive horseradish peroxidase-linked aptamer assay for sensitive detection of Aflatoxin B1. Talanta 2017; 179:344-349. [PMID: 29310242 DOI: 10.1016/j.talanta.2017.11.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 11/24/2022]
Abstract
Aflatoxin B1 (AFB1) is one of highly toxic mycotoxins and a known human carcinogen. The frequent contamination of AFB1 in food products and large health risk of AFB1 have raised global concerns. Sensitive detection of AFB1 is of vital importance and highly demanded. Herein, we reported a competitive horseradish peroxidase (HRP)-linked aptamer assay for AFB1, combining the advantages of aptamer for affinity binding and enzyme label for signal amplification. In this assay, free AFB1 in solution competed with a covalent conjugate of bovine serum albumin-AFB1 (BSA-AFB1) coated on the wells of microplate in binding to the HRP-labeled aptamer probe. HRP attached on BSA-AFB1 in the wells catalyzed the conversion of substrates into products, allowing the final detection of AFB1 through measurement of the generated products. When TMB (3,3',5,5'-tetramethylbenzidine dihydrochloride) was used as substrate, absorbance analysis of the product of enzyme reaction enabled the detection of AFB1 at 0.2nM. We further lowered the detection limit of AFB1 to 0.01nM through chemiluminescence analysis by using chemiluminescence substrate of HRP. This assay enabled the detection of AFB1 in complex sample matrix, such as diluted white wine and maize flour. This assay provides a simple, sensitive and rapid method for AFB1 determination.
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Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine. Int J Mol Sci 2017; 18:ijms18102142. [PMID: 29036890 PMCID: PMC5666824 DOI: 10.3390/ijms18102142] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Aptamers are short DNA/RNA oligonucleotides capable of binding to target molecules with high affinity and specificity. The process of selecting an aptamer is called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Thanks to the inherit merits, aptamers have been used in a wide range of applications, including disease diagnosis, targeted delivery agents and therapeutic uses. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, few aptamer-based products have already successfully entered into clinical and industrial use. Besides, it is still a challenge to obtain aptamers with high affinity in a more efficient way. Thus, it is important to comprehensively review the current shortage and achievement of aptamer-related technology. In this review, we first present the limitations and notable advances of aptamer selection. Then, we compare the different methods used in the kinetic characterization of aptamers. We also discuss the impetus and developments of the clinical application of aptamers.
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Malvano F, Albanese D, Pilloton R, Di Matteo M. A new label-free impedimetric aptasensor for gluten detection. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.03.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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An Aptamer-Based Biosensor for the Azole Class of Antifungal Drugs. mSphere 2017; 2:mSphere00274-17. [PMID: 28861519 PMCID: PMC5566834 DOI: 10.1128/msphere.00274-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/28/2017] [Indexed: 02/06/2023] Open
Abstract
This technical report describes the development of an aptamer for sensing azole antifungal drugs during therapeutic drug monitoring. Modified synthetic evolution of ligands through exponential enrichment (SELEX) was used to discover a DNA aptamer recognizing azole class antifungal drugs. This aptamer undergoes a secondary structural change upon binding to its target molecule, as shown through fluorescence anisotropy-based binding measurements. Experiments using circular dichroism spectroscopy revealed a unique G-quadruplex structure that was essential and specific for binding to the azole antifungal target. Aptamer-functionalized graphene field effect transistor (GFET) devices were created and used to measure the strength of binding of azole antifungals to this surface. In total, this aptamer and the supporting sensing platform provide a valuable tool for therapeutic drug monitoring of patients with invasive fungal infections. IMPORTANCE We have developed the first aptamer directed toward the azole class of antifungal drugs and a functional biosensor for these drugs. This aptamer has a unique secondary structure that allows it to bind to highly hydrophobic drugs. The aptamer works as a capture component of a graphene field effect transistor device. These devices can provide a quick and easy assay for determining drug concentrations. These will be useful for therapeutic drug monitoring of azole antifungal drugs, which is necessary to deal with the complex drug dosage profiles.
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Lin ZT, Gu J, Li CH, Lee TR, Xie L, Chen S, Cao PY, Jiang S, Yuan Y, Hong X, Wang H, Wang D, Wang X, Jiang GB, Heon M, Wu T. A Nanoparticle-Decorated Biomolecule-Responsive Polymer Enables Robust Signaling Cascade for Biosensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1702090. [PMID: 28612952 DOI: 10.1002/adma.201702090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/05/2017] [Indexed: 06/07/2023]
Abstract
To meet the increasing demands for ultrasensitivity in monitoring trace amounts of low-abundance early biomarkers or environmental toxins, the development of a robust sensing system is urgently needed. Here, a novel signal cascade strategy is reported via an ultrasensitive polymeric sensing system (UPSS) composed of gold nanoparticle (gNP)-decorated polymer, which enables gNP aggregation in polymeric network and electrical conductance change upon specific aptamer-based biomolecular recognition. Ultralow concentrations of thrombin (10-18 m) as well as a low molecular weight anatoxin (165 Da, 10-14 m) are detected selectively and reproducibly. The biomolecular recognition induced polymeric network shrinkage responses as well as dose-dependent responses of the UPSS are validated using in situ real-time atomic-force microscopy, representing the first instance of real-time detection of biomolecular binding-induced polymer shrinkage in soft matter. Furthermore, in situ real-time confocal laser scanning microscopy imaging reveals the dynamic process of gNP aggregation responses upon biomolecular binding.
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Affiliation(s)
- Zuan-Tao Lin
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Jianhua Gu
- Electron Microscopy Core, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Chien-Hung Li
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - T Randall Lee
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Lixin Xie
- Department of Physics and TcSUH, University of Houston, Houston, TX, 77204, USA
| | - Shuo Chen
- Department of Physics and TcSUH, University of Houston, Houston, TX, 77204, USA
| | - Piao-Yang Cao
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Jiang
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Yulin Yuan
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Xia Hong
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Hongting Wang
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Dezhi Wang
- Department of Physics and TcSUH, University of Houston, Houston, TX, 77204, USA
| | - Xifan Wang
- Department of Materials Science and NanoEngineering, Rice University, TX, 77005, USA
| | - Gang-Biao Jiang
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
- College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China
| | - Mikala Heon
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
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Aptamer-assisted novel technologies for detecting bacterial pathogens. Biomed Pharmacother 2017; 93:737-745. [PMID: 28700978 DOI: 10.1016/j.biopha.2017.07.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Nowadays, all people are at risk of infectious diseases that are mainly caused by bacteria causing infection. There is a permanent demand for an appropriate detection method that is affordable, practical, careful, rapid, sensitive, efficient and economical. Aptamers are single stranded DNA or RNA oligonucleotides, which can be recognized specifically and bind to their target molecules and also, be exploited in diagnostic applications. Recently, aptamer-based systems have offered great potentials in applications for the recognition of several important bacterial pathogens from clinical and food specimens. There are several reports appraising the diagnostic applicability of aptamer-based systems for the detection of pathogens. As for its excellent sensitivity, as well as its rapid and efficient detectability, this technique may be practical to indicate bacterial targets with less sample size and may consume less time than traditional methods These systems offer a promising approach for the sensitive and quick detection of food-borne and clinical agents. This review provides an overview of aptamer-based methods as a novel approach for detecting bacterial pathogens.
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85
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Sulatskaya AI, Rodina NP, Povarova OI, Kuznetsova IM, Turoverov KK. Different conditions of fibrillogenesis cause polymorphism of lysozyme amyloid fibrils. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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86
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Fluorescent sensor assay for β-lactamase in milk based on a combination of aptamer and graphene oxide. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.09.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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87
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Scoville DJ, Uhm TKB, Shallcross JA, Whelan RJ. Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing. J Nucleic Acids 2017; 2017:9879135. [PMID: 28280637 PMCID: PMC5322571 DOI: 10.1155/2017/9879135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/16/2017] [Indexed: 11/17/2022] Open
Abstract
CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman's risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg2+ ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target.
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Affiliation(s)
- Delia J. Scoville
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Tae Kyu Brian Uhm
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Jamie A. Shallcross
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Rebecca J. Whelan
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
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88
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Urmann K, Reich P, Walter JG, Beckmann D, Segal E, Scheper T. Rapid and label-free detection of protein a by aptamer-tethered porous silicon nanostructures. J Biotechnol 2017; 257:171-177. [PMID: 28131857 DOI: 10.1016/j.jbiotec.2017.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023]
Abstract
Protein A, which is secreted by and displayed on the cell membrane of Staphylococcus aureus is an important biomarker for S. aureus. Thus, its rapid and specific detection may facilitate the pathogen identification and initiation of proper treatment. Herein, we present a simple, label-free and rapid optical biosensor enabling specific detection of protein A. Protein A-binding aptamer serves as the capture probe and is immobilized onto a nanostructured porous silicon thin film, which serves as the optical transducer element. We demonstrate high sensitivity of the biosensor with a linear detection range between 8 and 23μM. The apparent dissociation constant was determined as 13.98μM and the LoD is 3.17μM. Harnessing the affinity between protein A and antibodies, a sandwich assay format was developed to amplify the optical signal associated with protein A capture by the aptamer. Using this approach, we increase the sensitivity of the biosensor, resulting in a three times lower LoD.
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Affiliation(s)
- Katharina Urmann
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hanover, Germany; Department of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Technion City, 32000 Haifa, Israel
| | - Peggy Reich
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hanover, Germany; Institute for Bioprocessing and Analytical Measurement Techniques e.V., Rosenhof, 37308 Heilbad Heiligenstadt, Germany
| | - Johanna-Gabriela Walter
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hanover, Germany
| | - Dieter Beckmann
- Institute for Bioprocessing and Analytical Measurement Techniques e.V., Rosenhof, 37308 Heilbad Heiligenstadt, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Technion City, 32000 Haifa, Israel.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hanover, Germany.
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89
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Sharma TK, Bruno JG, Dhiman A. ABCs of DNA aptamer and related assay development. Biotechnol Adv 2017; 35:275-301. [PMID: 28108354 DOI: 10.1016/j.biotechadv.2017.01.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/19/2016] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
This review is intended to guide the novice in aptamer research and development to understand virtually all of the aptamer development options and currently available assay modalities. Aptamer development topics range from discussions of basic and advanced versions of Systematic Evolution of Ligands by EXponential Enrichment (SELEX) and SELEX variations involving incorporation of exotic unnatural nucleotides to expand library diversity for even greater aptamer affinity and specificity to improved next generation methods of DNA sequencing, screening and tracking aptamer development throughout the SELEX process and characterization of lead aptamer candidates. Aptamer assay development topics include descriptions of various colorimetric and fluorescent assays in microplates or on membranes including homogeneous beacon and multiplexed Fluorescence Resonance Energy Transfer (FRET) assays. Finally, a discussion of the potential for marketing successful aptamer-based assays or test kits is included.
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Affiliation(s)
- Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India; AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Haryana 121001, India.
| | - John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite, 230, San Antonio, TX 78229, USA..
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India.; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
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90
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Entzian C, Schubert T. Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis. J Vis Exp 2017. [PMID: 28117825 DOI: 10.3791/55070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Characterization of molecular interactions in terms of basic binding parameters such as binding affinity, stoichiometry, and thermodynamics is an essential step in basic and applied science. MicroScale Thermophoresis (MST) is a sensitive biophysical method to obtain this important information. Relying on a physical effect called thermophoresis, which describes the movement of molecules through temperature gradients, this technology allows for the fast and precise determination of binding parameters in solution and allows the free choice of buffer conditions (from buffer to lysates/sera). MST uses the fact that an unbound molecule displays a different thermophoretic movement than a molecule that is in complex with a binding partner. The thermophoretic movement is altered in the moment of molecular interaction due to changes in size, charge, and hydration shell. By comparing the movement profiles of different molecular ratios of the two binding partners, quantitative information such as binding affinity (pM to mM) can be determined. Even challenging interactions between molecules of small sizes, such as aptamers and small compounds, can be studied by MST. Using the well-studied model interaction between the DH25.42 DNA aptamer and ATP, this manuscript provides a protocol to characterize aptamer-small molecule interactions. This study demonstrates that MST is highly sensitive and permits the mapping of the binding site of the 7.9 kDa DNA aptamer to the adenine of ATP.
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91
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Can Aptameric Ligands Specific to Plasma Coagulation Factor VII Bind the Recombinant Form with High Affinity: Affinity Measurement by Fluorescence Method. Avicenna J Med Biotechnol 2017; 9:109-112. [PMID: 28496951 PMCID: PMC5410128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Among diverse protein purification systems, affinity chromatography is the most attractive one in the purification process of coagulation factors. Coagulation factor VII is a plasma serine protease that has a significant role in natural human hemostasis and its recombinant form such as AryoSeven™, has been applied in clinical treatment of bleeding disorders. Immunoaffinity chromatography is the purification method of choice that is currently applied in the development of coagulation factor VIIa products. Aptamers as nucleic acid based affinity ligands are more promising than monoclonal antibodies. In addition, DNA aptamers are more acceptable than RNA ones in this regard. METHODS In this study, two of the aptameric DNA oligonucleotides that showed acceptable affinities for purification of coagulation factor VIIa from plasma, were selected to evaluate their affinity against Aryoseven. A serial dilution of fluorescence labeled aptamers was incubated against the concentration of 1 nM from Aryoseven. Then, a fluorescence index was calculated according to the fluorescence intensity data measured from test and control samples. The dissociation constant of aptamers was calculated according to the fluorescence index using Prism5 software. RESULTS Results showed that the binding affinity of the 44 nucleotide aptamer was more than 81 nucleotide aptamer sequence. As a result, this aptamer could be optimized in order to develop aptamer based affinity chromatography process for this form of recombinant coagulation factor VIIa. DISCUSSION Aptamers with shorter length of sequence could show higher affinity in target binding, as they could adapt more easily to suitable conformation according to target interaction. However, it should be considered that the selectivity of affinity ligands is also important for target purification and analytical applications.
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92
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Hu L, Wang L, Lu W, Zhai Q, Fan D, Liu X, Zhao J, Zhang H, Chen W. Selection, identification and application of DNA aptamers for the detection of Bifidobacterium breve. RSC Adv 2017. [DOI: 10.1039/c6ra27672e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the present study, a single-stranded DNA (ssDNA) aptamer binding toBifidobacterium brevewith high avidity and selectivity was selected through a whole-bacterium-based SELEX process.
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Affiliation(s)
- Lujun Hu
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Linlin Wang
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Daming Fan
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Xiaoming Liu
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- PR China
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93
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Lee M, Peterson BR. Quantification of Small Molecule-Protein Interactions using FRET between Tryptophan and the Pacific Blue Fluorophore. ACS OMEGA 2016; 1:1266-1276. [PMID: 28058293 PMCID: PMC5204206 DOI: 10.1021/acsomega.6b00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/06/2016] [Indexed: 05/14/2023]
Abstract
We report a new method to quantify the affinity of small molecules for proteins. This method is based on Förster resonance energy transfer (FRET) between endogenous tryptophan (Trp) residues and the coumarin-derived fluorophore Pacific Blue (PB). Tryptophan residues are frequently found in proteins near ligand-binding sites, making this approach potentially applicable to a wide range of systems. To improve access to PB, we developed a scalable multigram synthesis of this fluorophore, starting with inexpensive 2,3,4,5-tetrafluorobenzoic acid. This route was used to synthesize fluorescent derivatives of biotin, as well as lower affinity thiobiotin, iminobiotin, and imidazolidinethione analogues that bind the protein streptavidin. Compared with previously published FRET acceptors for tryptophan, PB proved to be superior in both sensitivity and efficiency. These unique properties of PB enabled direct quantification of dissociation constants (Kd) as well as competitive inhibition constants (Ki) in the micromolar to nanomolar range. In comparison to analogous binding studies using fluorescence polarization, fluorescence quenching, or fluorescence enhancement, affinities determined using Trp-FRET were more precise and accurate as validated using independent isothermal titration calorimetry studies. FRET between tryptophan and PB represents a new tool for the characterization of protein-ligand complexes.
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94
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Bayraç C, Öktem HA. Evaluation of Staphylococcus aureus DNA aptamer by enzyme-linked aptamer assay and isothermal titration calorimetry. J Mol Recognit 2016; 30. [PMID: 27696554 DOI: 10.1002/jmr.2583] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/06/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
To monitor the specificity of Staphylococcus aureus aptamer (SA-31) against its target cell, we used enzyme-linked aptamer assay. In the presence of target cell, horseradish peroxidase-conjugated streptavidin bound to biotin-labeled SA-31 showed specific binding to S aureus among 3 different bacteria with limit of detection of 103 colony-forming unit per milliliter. The apparent Ka was 1.39 μM-1 ± 0.3 μM-1 . The binding of SA-31 to membrane proteins extracted from cell surface was characterized using isothermal titration calorimetry, and the effect of changes in binding temperature and salt concentrations of binding buffer was evaluated based on thermodynamic parameters (Ka , ΔH, and ΔG). Since binding of aptamer to its targets solely depends on its 3-dimensional structure under experimental conditions used in selection process, the change in temperature and ion concentration changed the affinity of SA-31 to its target on surface of bacteria. At 4°C, SA-31 did not show an affinity to its target with poor heat change upon injection of membrane fraction to aptamer solution. However, the apparent association constants of SA-31 slightly varied from Ka = 1.56 μM-1 ± 0.69 μM-1 at 25°C to Ka = 1.03 μM-1 ± 0.9 μM-1 at 37°C. At spontaneously occurring exothermic binding reactions, affinities of S aureus aptamer to its target were also 9.44 μM-1 ± 0.38 μM-1 at 50mM, 1.60 μM-1 ± 0.11 μM-1 at 137mM, and 3.28 μM-1 ± 0.46 μM-1 at 200 mM of salt concentration. In this study, it was demonstrated that enzyme-linked aptamer assay and isothermal titration calorimetry were useful tools for studying the fundamental binding mechanism between a DNA aptamer and its target on the outer surface of S aureus.
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Affiliation(s)
- Ceren Bayraç
- Bioengineering Department, Karamanoğlu Mehmetbey University, Yunus Emre Campus, Karaman, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Hüseyin Avni Öktem
- Konya Food & Agriculture University, Dedekorkut Mah. Beyşehir Cad. No. 9, Konya, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
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95
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Soller KJ, Yang J, Veglia G, Bowser MT. Reversal of Phospholamban Inhibition of the Sarco(endo)plasmic Reticulum Ca2+-ATPase (SERCA) Using Short, Protein-interacting RNAs and Oligonucleotide Analogs. J Biol Chem 2016; 291:21510-21518. [PMID: 27531746 DOI: 10.1074/jbc.m116.738807] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/05/2016] [Indexed: 01/16/2023] Open
Abstract
The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) and phospholamban (PLN) complex regulates heart relaxation through its removal of cytosolic Ca2+ during diastole. Dysfunction of this complex has been related to many heart disorders and is therefore a key pharmacological target. There are currently no therapeutics that directly target either SERCA or PLN. It has been previously reported that single-stranded DNA binds PLN with strong affinity and relieves inhibition of SERCA in a length-dependent manner. In the current article, we demonstrate that RNAs and single-stranded oligonucleotide analogs, or xeno nucleic acids (XNAs), also bind PLN strongly (Kd <10 nm) and relieve inhibition of SERCA. Affinity for PLN is sequence-independent. Relief of PLN inhibition is length-dependent, allowing SERCA activity to be restored incrementally. The improved in vivo stability of XNAs offers more realistic pharmacological potential than DNA or RNA. We also found that microRNAs (miRNAs) 1 and 21 bind PLN strongly and relieve PLN inhibition of SERCA to a greater extent than a similar length random sequence RNA mixture. This may suggest that miR-1 and miR-21 have evolved to contain distinct sequence elements that are more effective at relieving PLN inhibition than random sequences.
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Affiliation(s)
| | - Jing Yang
- From the Departments of Chemistry and
| | - Gianluigi Veglia
- From the Departments of Chemistry and .,Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
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96
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Kim J, Olsen TR, Zhu J, Hilton JP, Yang KA, Pei R, Stojanovic MN, Lin Q. Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation. Sci Rep 2016; 6:26139. [PMID: 27217242 PMCID: PMC4877600 DOI: 10.1038/srep26139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/20/2016] [Indexed: 01/06/2023] Open
Abstract
We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the processes of affinity selection and amplification of target-binding oligonucleotides, and an electrophoretic DNA manipulation scheme for the coupling of these processes, which are required to occur in different buffers. This achieves the full microfluidic integration of SELEX, thereby enabling highly efficient isolation of aptamers in drastically reduced times and with minimized consumption of biological material. The approach as such also offers broad target applicability by allowing selection of aptamers with respect to targets that are either surface-immobilized or solution-borne, potentially allowing aptamers to be developed as readily available affinity reagents for a wide range of targets. We demonstrate the utility of this approach on two different procedures, respectively for isolating aptamers against a surface-immobilized protein (immunoglobulin E) and a solution-phase small molecule (bisboronic acid in the presence of glucose). In both cases aptamer candidates were isolated in three rounds of SELEX within a total process time of approximately 10 hours.
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Affiliation(s)
- Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Timothy R. Olsen
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - John P. Hilton
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Kyung-Ae Yang
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Columbia University, New York, NY 10032, United States
| | - Renjun Pei
- Division of Nanobiomedicine, Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China
| | - Milan N. Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Columbia University, New York, NY 10032, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
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97
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Heiat M, Najafi A, Ranjbar R, Latifi AM, Rasaee MJ. Computational approach to analyze isolated ssDNA aptamers against angiotensin II. J Biotechnol 2016; 230:34-9. [PMID: 27188956 DOI: 10.1016/j.jbiotec.2016.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022]
Abstract
Aptamers are oligonucleotides with highly structured molecules that can bind to their targets through specific 3-D conformation. Commonly, not all the nucleotides such as primer binding fixed region and some other sequences are vital for aptamers folding and interaction. Elimination of unnecessary regions needs trustworthy prediction tools to reduce experimental efforts and errors. Here we introduced a manipulated in-silico approach to predict the 3-D structure of aptamers and their target interactions. To design an approach for computational analysis of isolated ssDNA aptamers (FLC112, FLC125 and their truncated core region including CRC112 and CRC125), their secondary and tertiary structures were modeled by Mfold and RNA composer respectively. Output PDB files were modified from RNA to DNA in the discovery studio visualizer software. Using ZDOCK server, the aptamer-target interactions were predicted. Finally, the interaction scores were compared with the experimental results. In-silico interaction scores and the experimental outcomes were in the same descending arrangement of FLC112>CRC125>CRC112>FLC125 with similar intensity. The consistent results of innovative in-silico method with experimental outputs, affirmed that the present method may be a reliable approach. Also, it showed that the exact in-silico predictions can be utilized as a credible reference to find aptameric fragments binding potency.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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98
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Tan SY, Acquah C, Sidhu A, Ongkudon CM, Yon LS, Danquah MK. SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization. Crit Rev Anal Chem 2016; 46:521-37. [PMID: 26980177 DOI: 10.1080/10408347.2016.1157014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.
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Affiliation(s)
- Sze Y Tan
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Caleb Acquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Amandeep Sidhu
- b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia.,c Faculty of Health Sciences , Curtin University , Perth , Australia
| | - Clarence M Ongkudon
- d Biotechnology Research Institute , University Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
| | - L S Yon
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia
| | - Michael K Danquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
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99
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Aptamer-based 'point-of-care testing'. Biotechnol Adv 2016; 34:198-208. [PMID: 26876017 DOI: 10.1016/j.biotechadv.2016.02.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/06/2016] [Accepted: 02/07/2016] [Indexed: 12/13/2022]
Abstract
Aptamers are single-stranded oligonucleotides that can be artificially generated by a method called Systematic evolution of ligands by exponential enrichment (SELEX). The generated aptamers have been assessed for high-performance sensing applications due to their appealing characteristics. With either aptamers alone or complementing with antibodies, several high sensitive and portable sensors have been demonstrated for use in 'point-of-care testing'. Due to their high suitability and flexibility, aptamers are conjugated with nanostructures and utilized in field applications. Moreover, aptamers are more amenable to chemical modifications, making them capable of utilization with most developed sensors. In this overview, we discuss novel, portable, and aptamer-based sensing strategies that are suitable for 'point-of-care testing'.
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100
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Gao L, Ju L, Cui H. Determination of the binding constant of specific interactions and binding target concentration simultaneously using a general chemiluminescence method. RSC Adv 2016. [DOI: 10.1039/c5ra24928g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The measurement of the binding constant of specific interactions and concentration of a target is of considerable importance in clinical diagnosis, therapy, bioassays and drug design.
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Affiliation(s)
- Lingfeng Gao
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Chemistry
- University of Science & Technology of China
- Hefei
| | - Li Ju
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Chemistry
- University of Science & Technology of China
- Hefei
| | - Hua Cui
- CAS Key Laboratory of Soft Matter Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials
- Department of Chemistry
- University of Science & Technology of China
- Hefei
| |
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