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Cho H, Oh DE, Côté S, Lee CS, Kim TH. Orientation-Guided Immobilization of Probe DNA on swCNT-FET for Enhancing Sensitivity of EcoRV Detection. NANO LETTERS 2024; 24:1901-1908. [PMID: 38147528 DOI: 10.1021/acs.nanolett.3c03877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
We present a novel approach that integrates electrical measurements with molecular dynamics (MD) simulations to assess the activity of type-II restriction endonucleases, specifically EcoRV. Our approach employs a single-walled carbon nanotube field-effect transistor (swCNT-FET) functionalized with the EcoRV substrate DNA, enabling the detection of enzymatic cleavage events. Notably, we leveraged the methylene blue (MB) tag as an "orientation guide" to immobilize the EcoRV substrate DNA in a specific direction, thereby enhancing the proximity of the DNA cleavage reaction to the swCNT surface and consequently improving the sensitivity in EcoRV detection. We conducted computational modeling to compare the conformations and electrostatic potential (ESP) of MB-tagged DNA with its MB-free counterpart, providing strong support for our electrical measurements. Both conformational and ESP simulations exhibited robust agreement with our experimental data. The inhibitory efficacy of the EcoRV inhibitor aurintricarboxylic acid (ATA) was also evaluated, and the selectivity of the sensing device was examined.
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Affiliation(s)
- Hyunju Cho
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Da Eun Oh
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal H2 V 0B3, Canada
- Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme J7Z 4 V2, Canada
| | - Chang-Seuk Lee
- Department of Chemistry, Seoul Women's University, Seoul 01797, Republic of Korea
| | - Tae Hyun Kim
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
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Oh DE, Kim HB, Kim TH. Electrochemical DNA Cleavage Sensing for EcoRV Activity and Inhibition with an ERGO Electrode. BIOSENSORS 2024; 14:73. [PMID: 38391992 PMCID: PMC10886839 DOI: 10.3390/bios14020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
An electrochemically reduced graphene oxide (ERGO) electrode-based electrochemical assay was developed for rapid, sensitive, and straightforward analysis of both activity and inhibition of the endonuclease EcoRV. The procedure uses a DNA substrate designed for EcoRV, featuring a double-stranded DNA (dsDNA) region labeled with methylene blue (MB) and a single-stranded DNA (ssDNA) region immobilized on the ERGO surface. The ERGO electrode, immobilized with the DNA substrate, was subsequently exposed to a sample containing EcoRV. Upon enzymatic hydrolysis, the cleaved dsDNA fragments were detached from the ERGO surface, leading to a decrease in the MB concentration near the electrode. This diminished the electron transfer efficiency for MB reduction, resulting in a decreased reduction current. This assay demonstrates excellent specificity and high sensitivity, with a limit of detection (LOD) of 9.5 × 10-3 U mL-1. Importantly, it can also measure EcoRV activity in the presence of aurintricarboxylic acid, a known inhibitor, highlighting its potential for drug discovery and clinical diagnostic applications.
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Affiliation(s)
| | | | - Tae Hyun Kim
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea; (D.E.O.); (H.B.K.)
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Wang Y, Li H, Zhou J, Wang F, Qian Y, Fu L. An antifouling polydopamine-based fluorescent aptasensor for determination of arginine kinase. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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Lee CY, Liao CH, Fang NM, Hsieh YZ. DNAzyme-Amplified Label-Free Biosensor for the Simple and Sensitive Detection of Pyrophosphatase. BIOSENSORS 2021; 11:422. [PMID: 34821638 PMCID: PMC8615721 DOI: 10.3390/bios11110422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The level of pyrophosphatase (PPase) expression has been suggested as a potential biomarker of various cancers, and its prognostic value has been evaluated in patients suffering from lung cancer, colorectal cancer, and hyperthyroidism. However, the detection of PPase usually needs specific materials that require complicated, time-consuming reactions with restricted linear range and sensitivity, limiting their application in early clinical diagnosis. Herein, we developed a DNAzyme-based biosensor for the detection of PPase. In the presence of PPase, pyrophosphate (PPi) and Cu2+ ions released from the PPi-Cu2+-PPi complex induce the cleavage of the DNAzyme and the corresponding substrate. An apurinic/apyrimidinic (AP) site was elaborately designed within substrates that could encase the fluorophore 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND). The fluorescence of ATMND was initially quenched but restored when the DNAzyme/substrate complex was hydrolyzed with the release of ATMND. In this way, the PPase activity can be estimated by detecting the increased fluorescence of the released ATMND. Under optimized conditions, the activity of PPase could be analyzed at concentrations from 0.5 to 1000 mU, with the lowest detectable concentration being 0.5 mU. This work lays a foundation for developing a DNAzyme-amplified fluorescent biosensor with a high sensitivity, a wide linear range, and single-step operation for use as an easy diagnostic for PPase analysis.
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Affiliation(s)
- Cheng-Yu Lee
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - Chi-Hsiang Liao
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - Nei-Mei Fang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
| | - You-Zung Hsieh
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (C.-Y.L.); (C.-H.L.); (N.-M.F.)
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
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Yim Y, Shin H, Ahn SM, Min DH. Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery. Chem Commun (Camb) 2021; 57:9820-9833. [PMID: 34494621 DOI: 10.1039/d1cc02157e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.
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Affiliation(s)
- Yeajee Yim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Min Ahn
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
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Guo R, Wang DN, Wei YY, Zhang YZ, Yang CG, Xu ZR. Colloidal photonic crystal array chip based on nanoparticle self-assembly on patterned hydrophobic surface for signal-enhanced fluorescent assay of adenosine. Mikrochim Acta 2020; 187:194. [DOI: 10.1007/s00604-020-4164-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022]
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Lee J, Purushothaman B, Song JM. Inkjet Bioprinting on Parchment Paper for Hit Identification from Small Molecule Libraries. ACS OMEGA 2020; 5:588-596. [PMID: 31956806 PMCID: PMC6964283 DOI: 10.1021/acsomega.9b03169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
In this study, an inkjet bioprinting-based high-throughput screening (HTS) system was designed and applied for the first time to a catecholpyrimidine-based small molecule library to find hit compounds that inhibit c-Jun NH2-terminal kinase1 (JNK1). JNK1 kinase, inactivated MAPKAPK2, and specific fluorescent peptides along with bioink were printed on parchment paper under optimized printing conditions that did not allow rapid evaporation of printed media based on Triton-X and glycerol. Subsequently, different small compounds were printed and tested against JNK1 kinase to evaluate their degree of phosphorylation inhibition. After printing and incubation, fluorescence intensities from the phosphorylated/nonphosphorylated peptide were acquired for the % phosphorylation analysis. The IM50 (inhibitory mole 50) value was determined as 1.55 × 10-15 mol for the hit compound, 22. Thus, this work demonstrated that inkjet bioprinting-based HTS can potentially be adopted for the drug discovery process using small molecule libraries, and cost-effective HTS can be expected to be established based on its low nano- to picoliter printing volume.
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Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014-2019). Mikrochim Acta 2019; 186:563. [PMID: 31338623 DOI: 10.1007/s00604-019-3659-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Abstract
Fluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field. Graphical abstract Schematic representation of a fluorescence resonance energy transfer-based aptamer nanoprobe in the absence and presence of a given target molecule (analyte). Structures are not drawn to their original scales.
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A review on advances in methods for modification of paper supports for use in point-of-care testing. Mikrochim Acta 2019; 186:521. [DOI: 10.1007/s00604-019-3626-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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