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Zhou K, Zhou J, Cao S, Zheng Y, Zhang XY, Chen C, Zhang XE, Men D. Bifunctional Protein TC1 Mediated One-Pot Strategy for Robust Immobilization of DNA with High Accessibility. SMALL METHODS 2024:e2400049. [PMID: 38804235 DOI: 10.1002/smtd.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/24/2024] [Indexed: 05/29/2024]
Abstract
Immobilizing DNA with high accessibility at the interface is attractive but challenging. Current methods often involve multiple chemical reactions and derivatives. In this study, an endonuclease, TC1, is introduced to develop a robust strategy for immobilizing DNA with enhanced accessibility. TC1 enables direct immobilization of DNA onto a solid support through self-catalytic DNA covalent coupling and robust solid adsorption capabilities. This method demonstrates high accessibility to target molecules, supported by the improved sensitivity of DNA hybridization and aptamer-target recognition assays. TC1-mediated DNA immobilization is a one-pot reaction that does not require chemical derivatives, making it promising for the development of high-performance DNA materials and technologies.
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Affiliation(s)
- Kun Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shanshan Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Ying Zheng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xin-Yu Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Chen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen university of Advanced Technology, Shenzhen, 518055, P. R. China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
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2
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Ulyashova MM, Presnova GV, Filippova AA, Grigorenko VG, Egorov AM, Rubtsova MY. Multiplex Microarrays in 96-Well Plates Photoactivated with 4-Azidotetrafluorobenzaldehyde for the Identification and Quantification of β-Lactamase Genes and Their RNA Transcripts. Curr Issues Mol Biol 2023; 46:53-66. [PMID: 38275665 PMCID: PMC10814224 DOI: 10.3390/cimb46010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Antibiotic-resistant bacteria represent a global issue that calls for novel approaches to diagnosis and treatment. Given the variety of genetic factors that determine resistance, multiplex methods hold promise in this area. We developed a novel method to covalently attach oligonucleotide probes to the wells of polystyrene plates using photoactivation with 4-azidotetrafluorobenzaldehyde. Then, it was used to develop the technique of microarrays in the wells. It consists of the following steps: activating polystyrene, hybridizing the probes with biotinylated target DNA, and developing the result using a streptavidin-peroxidase conjugate with colorimetric detection. The first microarray was designed to identify 11 different gene types and 16 single-nucleotide polymorphisms (SNPs) of clinically relevant ESBLs and carbapenemases, which confer Gram-negative bacteria resistance to β-lactam antibiotics. The detection of bla genes in 65 clinical isolates of Enterobacteriaceae demonstrated the high sensitivity and reproducibility of the technique. The highly reproducible spot staining of colorimetric microarrays allowed us to design a second microarray that was intended to quantify four different types of bla mRNAs in order to ascertain their expressions. The combination of reliable performance, high throughput in standard 96-well plates, and inexpensive colorimetric detection makes the microarrays suitable for routine clinical application and for the study of multi-drug resistant bacteria.
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Affiliation(s)
| | | | | | | | | | - Maya Yu. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.M.U.); (G.V.P.); (A.A.F.); (V.G.G.); (A.M.E.)
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3
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Omidfar K, Riahi F, Kashanian S. Lateral Flow Assay: A Summary of Recent Progress for Improving Assay Performance. BIOSENSORS 2023; 13:837. [PMID: 37754072 PMCID: PMC10526804 DOI: 10.3390/bios13090837] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023]
Abstract
Lateral flow tests are one of the most important types of paper-based point-of-care (POCT) diagnostic tools. It shows great potential as an implement for improving the rapid screening and management of infections in global pandemics or other potential health disorders by using minimally expert staff in locations where no sophisticated laboratory services are accessible. They can detect different types of biomarkers in various biological samples and provide the results in a little time at a low price. An important challenge regarding conventional LFAs is increasing their sensitivity and specificity. There are two main approaches to increase sensitivity and specificity, including assay improvement and target enrichment. Assay improvement comprises the assay optimization and signal amplification techniques. In this study, a summarize of various sensitivity and specificity enhancement strategies with an objective evaluation are presented, such as detection element immobilization, capillary flow rate adjusting, label evolution, sample extraction and enrichment, etc. and also the key findings in improving the LFA performance and solving their limitations are discussed along with numerous examples.
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Affiliation(s)
- Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular—Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran 1458889694, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran 1458889694, Iran
| | - Fatemeh Riahi
- Biosensor Research Center, Endocrinology and Metabolism Molecular—Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran 1458889694, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran 1458889694, Iran
| | - Soheila Kashanian
- Faculty of Chemistry, Razi University, Kermanshah 6714414971, Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran
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4
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Martorell S, Maquieira Á, Tortajada-Genaro LA. A genosensor for detecting single-point mutations in dendron chips after blocked recombinase polymerase amplification. Analyst 2022; 147:2180-2188. [DOI: 10.1039/d2an00160h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dendron–probe conjugates were effectively immobilized on chip surfaces, improving assay sensitivity and simplifying coupling reactions. Combined with an isothermal amplification, the array method accurately detects single-base changes.
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Affiliation(s)
- Sara Martorell
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Valencia, Spain
- Chemistry department, Universitat Politècnica de València, Valencia, Spain
| | - Luis A. Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Valencia, Spain
- Chemistry department, Universitat Politècnica de València, Valencia, Spain
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5
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Tellez-Cruz MM, Escorihuela J, Solorza-Feria O, Compañ V. Proton Exchange Membrane Fuel Cells (PEMFCs): Advances and Challenges. Polymers (Basel) 2021; 13:3064. [PMID: 34577965 PMCID: PMC8468942 DOI: 10.3390/polym13183064] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/21/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
The study of the electrochemical catalyst conversion of renewable electricity and carbon oxides into chemical fuels attracts a great deal of attention by different researchers. The main role of this process is in mitigating the worldwide energy crisis through a closed technological carbon cycle, where chemical fuels, such as hydrogen, are stored and reconverted to electricity via electrochemical reaction processes in fuel cells. The scientific community focuses its efforts on the development of high-performance polymeric membranes together with nanomaterials with high catalytic activity and stability in order to reduce the platinum group metal applied as a cathode to build stacks of proton exchange membrane fuel cells (PEMFCs) to work at low and moderate temperatures. The design of new conductive membranes and nanoparticles (NPs) whose morphology directly affects their catalytic properties is of utmost importance. Nanoparticle morphologies, like cubes, octahedrons, icosahedrons, bipyramids, plates, and polyhedrons, among others, are widely studied for catalysis applications. The recent progress around the high catalytic activity has focused on the stabilizing agents and their potential impact on nanomaterial synthesis to induce changes in the morphology of NPs.
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Affiliation(s)
- Miriam M. Tellez-Cruz
- Department of Chemistry, Centro de Investigación y de Estudios Avanzados, Av. IPN 2508, Ciudad de México 07360, Mexico; (M.M.T.-C.); (O.S.-F.)
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, Av. Vicent Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - Omar Solorza-Feria
- Department of Chemistry, Centro de Investigación y de Estudios Avanzados, Av. IPN 2508, Ciudad de México 07360, Mexico; (M.M.T.-C.); (O.S.-F.)
| | - Vicente Compañ
- Departamento de Termodinámica Aplicada (ETSII), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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6
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Affinity‐switchable
biotin probes for the analysis of enzymes and small reactive molecules on microarray platform. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Sy Piecco KWE, Vicente JR, Pyle JR, Ingram DC, Kordesch ME, Chen J. Reusable Chemically-Micropatterned Substrates via Sequential Photoinitiated Thiol-Ene Reactions as Template for Perovskite Thin-Film Microarrays. ACS APPLIED ELECTRONIC MATERIALS 2019; 1:2279-2286. [PMID: 32832905 PMCID: PMC7442211 DOI: 10.1021/acsaelm.9b00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Patterning semiconducting materials are important for many applications such as microelectronics, displays, and photodetectors. Lead halide perovskites are an emerging class of semiconducting materials that can be patterned via solution-based methods. Here we report an all-benchtop patterning strategy by first generating a patterned surface with contrasting wettabilities to organic solvents that have been used in the perovskite precursor solution then spin-coating the solution onto the patterned surface. The precursor solution only stays in the area with higher affinity (wettability). We applied sequential sunlight-initiated thiol-ene reactions to functionalize (and pattern) both glass and conductive fluorine-doped tin oxide (FTO) transparent glass surfaces. The functionalized surfaces were measured with the solvent contact angles of water and different organic solvents and were further characterized by XPS, selective fluorescence staining, and selective DNA adsorption. By simply spin-coating and baking the perovskite precursor solution on the patterned substrates, we obtained perovskite thin-film microarrays. The spin-coated perovskite arrays were characterized by XRD, AFM, and SEM. We concluded that patterned substrate prepared via sequential sunlight-initiated thiol-ene click reactions is suitable to fabricate perovskite arrays via the benchtop process. In addition, the same patterned substrates can be reused several times until a favorable perovskite microarray is acquired. Among a few conditions we have tested, DMSO solvent and modified FTO surfaces with alternatively carboxylic acid and alkane is the best combination to obtain high-quality perovskite microarrays. The solvent contact angle of DMSO on carboxylic acid-modified FTO surface is nearly zero and 65±3° on octadecane modified FTO surface.
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Affiliation(s)
- Kurt Waldo E. Sy Piecco
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
- University of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Juvinch R. Vicente
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
- University of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Joseph R. Pyle
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - David C. Ingram
- Department of Physics and Astronomy, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Martin E. Kordesch
- Department of Physics and Astronomy, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
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8
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Huertas CS, Calvo-Lozano O, Mitchell A, Lechuga LM. Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective. Front Chem 2019; 7:724. [PMID: 31709240 PMCID: PMC6823211 DOI: 10.3389/fchem.2019.00724] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.
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Affiliation(s)
- Cesar S. Huertas
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
| | - Arnan Mitchell
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
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9
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Díaz-Betancor Z, Bañuls MJ, Maquieira Á. Photoclick chemistry to create dextran-based nucleic acid microarrays. Anal Bioanal Chem 2019; 411:6745-6754. [PMID: 31482291 DOI: 10.1007/s00216-019-02050-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
Abstract
In the literature, there are reports of the utilization of various hydrogels to create generic platforms for protein microarray applications. Here, a novel strategy was developed to obtain high-performance microarrays. In it, a dextran hydrogel is used to covalently immobilize oligonucleotides and proteins. This method employs aqueous solutions of dextran methacrylate (Dx-MA), which is a biocompatible photopolymerizable monomer. Capture probes are immobilized inside the hydrogel via a light-induced thiol-acrylate coupling reaction at the same time as the dextran polymer is formed. Hydrogel microarrays based on this technique were prepared on different surfaces, such as a Blu-ray Disk and polycarbonate or alkene-functionalized glass slides, and these systems showed high probe-loading capabilities and good biorecognition yields. This methodology presents advantages such as a low cost, a short analysis time, a low limit of detection, and multiplexing capabilities, among others. Confocal fluorescence microscopy analysis demonstrated that in these hydrogel-based microarrays, receptor immobilization and the biorecognition event occurred within the hydrogel and not merely on the surface.
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Affiliation(s)
- Zeneida Díaz-Betancor
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - María-José Bañuls
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. .,Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Ángel Maquieira
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
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10
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Phosphorylcholine-based hydrogel for immobilization of biomolecules. Application to fluorometric microarrays for use in hybridization assays and immunoassays, and nanophotonic biosensing. Mikrochim Acta 2019; 186:570. [DOI: 10.1007/s00604-019-3691-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/07/2019] [Indexed: 12/11/2022]
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11
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Jiménez-Meneses P, Bañuls MJ, Puchades R, Maquieira Á. Novel and rapid activation of polyvinylidene fluoride membranes by UV light. REACT FUNCT POLYM 2019. [DOI: 10.1016/j.reactfunctpolym.2019.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Nonkumwong J, Erasquin UJ, Sy Piecco KW, Premadasa UI, Aboelenen AM, Tangonan A, Chen J, Ingram D, Srisombat L, Cimatu KLA. Successive Surface Reactions on Hydrophilic Silica for Modified Magnetic Nanoparticle Attachment Probed by Sum-Frequency Generation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:12680-12693. [PMID: 30300547 DOI: 10.1021/acs.langmuir.8b01333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Successive surface reactions on hydrophilic silica substrates were designed and performed to immobilize ethanolamine-modified magnetic ferrite-based nanoparticle (NP) for surface characterization. The various surfaces were monitored using sum-frequency generation (SFG) spectroscopy. The surface of the hydrophilic quartz substrate was first converted to a vinyl-terminated surface by utilizing a silanization reaction, and then, the surface functional groups were converted to carboxylic-terminated groups via a thiol-ene reaction. The appearance and disappearance of the vinyl (═CH2) peak at ∼2990 cm-1 in the SFG spectra were examined to confirm the success of the silanization and thiol-ene reactions, respectively. Acyl chloride (-COCl) formation from carboxy (-COOH) functional group was then performed for further attachment of magnetic amine-functionalized magnesium ferrite nanoparticles (NPs) via amide bond formation. The scattered NPs attached on the modified silica substrate was then used to study the changes in the spectral profile of the ethanolamine modifier of the NPs for in situ lead(II) (Pb2+) adsorption at the solid-liquid interface using SFG spectroscopy. However, due to the limited number of NPs attached and sensitivity of SFG spectroscopy toward expected change in the modifier spectroscopically, no significant change was observed in the SFG spectrum of the modified silica with magnetic NPs during exposure to Pb2+ solution. Nevertheless, SFG spectroscopy as a surface technique successfully monitored the modifications from a clean fused substrate to -COCl formation that was used to immobilize the decorated magnetic nanoparticles. The method developed in this study can provide a reference for many surface or interfacial studies important for selective attachment of adsorbed organic or inorganic materials or particles.
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Affiliation(s)
- Jeeranan Nonkumwong
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
- Department of Chemistry, Faculty of Science , Chiang Mai University , Chiang Mai 50200 , Thailand
| | - Uriel Joseph Erasquin
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Kurt Waldo Sy Piecco
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Uvinduni I Premadasa
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Ahmed M Aboelenen
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Andrew Tangonan
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Jixin Chen
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - David Ingram
- Department of Physics and Astronomy , Ohio University , 139 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
| | - Laongnuan Srisombat
- Department of Chemistry, Faculty of Science , Chiang Mai University , Chiang Mai 50200 , Thailand
| | - Katherine Leslee Asetre Cimatu
- Department of Chemistry and Biochemistry , Ohio University , 100 University Terrace, 136 Clippinger Laboratories , Athens , Ohio 45701-2979 , United States
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13
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Jiménez-Meneses P, Bañuls MJ, Puchades R, Maquieira Á. Fluor-thiol Photocoupling Reaction for Developing High Performance Nucleic Acid (NA) Microarrays. Anal Chem 2018; 90:11224-11231. [DOI: 10.1021/acs.analchem.8b00265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Pilar Jiménez-Meneses
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - María-José Bañuls
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rosa Puchades
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Departamento de Química, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
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14
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Flamme M, Clarke E, Gasser G, Hollenstein M. Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives. Molecules 2018; 23:E1515. [PMID: 29932443 PMCID: PMC6099586 DOI: 10.3390/molecules23071515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as electron transfer or the construction of nanomaterials. Among the different metal complexes coupled to oligonucleotides, ruthenium complexes, have been extensively studied due to their remarkable properties. The resulting DNA-ruthenium bioconjugates have already demonstrated their potency in numerous applications. Consequently, this review focuses on the recent synthetic methods developed for the preparation of ruthenium complexes covalently linked to oligonucleotides. In addition, the usefulness of such conjugates will be highlighted and their applications from nanotechnologies to therapeutic purposes will be discussed.
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Affiliation(s)
- Marie Flamme
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Emma Clarke
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Gilles Gasser
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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15
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Röthlisberger P, Levi-Acobas F, Sarac I, Baron B, England P, Marlière P, Herdewijn P, Hollenstein M. Facile immobilization of DNA using an enzymatic his-tag mimic. Chem Commun (Camb) 2018; 53:13031-13034. [PMID: 29164188 DOI: 10.1039/c7cc07207d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methods for immobilization of DNA on solid supports are in high demand. Herein, we present a generally applicable enzymatic method for the immobilization of DNA without any prior chemical derivatization. This strategy relies on the homopolymerization of the modified triphosphate dImTP by the TdT. The resulting enzymatic his-tag mimic ensures binding of DNA on Ni-NTA agarose. The usefulness of this method is highlighted by the immobilization of functional nucleic acids without impairing their specific activities.
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Affiliation(s)
- Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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16
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Love DM, Kim K, Goodrich JT, Fairbanks BD, Worrell BT, Stoykovich MP, Musgrave CB, Bowman CN. Amine Induced Retardation of the Radical-Mediated Thiol-Ene Reaction via the Formation of Metastable Disulfide Radical Anions. J Org Chem 2018; 83:2912-2919. [PMID: 29390175 DOI: 10.1021/acs.joc.8b00143] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The effect of amines on the kinetics and efficacy of radical-mediated thiol-ene coupling (TEC) reactions was investigated. By varying the thiol reactant and amine additive, it was shown that amines retard thiyl radical-mediated reactions when the amine is adequately basic enough to deprotonate the thiol affording the thiolate anion, e.g., when the weakly basic amine tetramethylethylenediamine was incorporated in the TEC reaction between butyl 2-mercaptoacetate and an allyl ether at 5 mol %, the final conversion was reduced from quantitative to <40%. Alternatively, no effect is observed when the less acidic thiol butyl 3-mercaptopropionate is employed. The thiolate anion was established as the retarding species through the introduction of ammonium and thiolate salt additives into TEC formulations. The formation of a two-sulfur three-electron bonded disulfide radical anion (DRA) species by the reaction of a thiyl radical with a thiolate anion was determined as the cause for the reduction in catalytic radicals and the TEC rate. Thermodynamic and kinetic trends in DRA formations were computed using density functional theory and by modeling the reaction as an associative electron transfer process. These trends correlate well with the experimental retardation trends of various thiolate anions in TEC reactions.
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Affiliation(s)
| | | | | | | | | | - Mark P Stoykovich
- The Institute for Molecular Engineering, The University of Chicago , Chicago Illinois, 60637, United States
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17
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Alonso R, Jiménez-Meneses P, García-Rupérez J, Bañuls MJ, Maquieira Á. Thiol–ene click chemistry towards easy microarraying of half-antibodies. Chem Commun (Camb) 2018; 54:6144-6147. [DOI: 10.1039/c8cc01369a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
UV light catalyses in a few seconds the thiol–ene coupling reaction between half-antibodies and vinyl functionalized surfaces, providing high performance microarrays.
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Affiliation(s)
- Rafael Alonso
- Departamento de Química
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València
- Universitat de València
- Valencia
| | - Pilar Jiménez-Meneses
- Departamento de Química
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València
- Universitat de València
- Valencia
| | | | - María-José Bañuls
- Departamento de Química
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València
- Universitat de València
- Valencia
| | - Ángel Maquieira
- Departamento de Química
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València
- Universitat de València
- Valencia
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18
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Clark KD, Varona M, Anderson JL. Ion‐Tagged Oligonucleotides Coupled with a Magnetic Liquid Support for the Sequence‐Specific Capture of DNA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin D. Clark
- Department of Chemistry Iowa State University Ames IA 50011 USA
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19
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Clark KD, Varona M, Anderson JL. Ion-Tagged Oligonucleotides Coupled with a Magnetic Liquid Support for the Sequence-Specific Capture of DNA. Angew Chem Int Ed Engl 2017; 56:7630-7633. [PMID: 28464345 DOI: 10.1002/anie.201703299] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Indexed: 12/30/2022]
Abstract
The isolation of specific nucleic acid sequences is a major bottleneck in molecular diagnostics. Magnetic beads/particles are typically used as solid supports for the capture of DNA targets to improve sample throughput but aggregate over time resulting in lower capture efficiency and obstruction of liquid handling devices. Herein, we describe a particle-free approach to sequence-specific DNA extraction using a magnetic liquid support and ion-tagged oligonucleotide (ITO) probes. ITO conjugates were synthesized with the highest yields ever achieved for the radical thiol-ene coupling of a substrate and oligonucleotide. In addition to distinguishing nucleotide mismatches, the ITO and magnetic liquid-based approach was more sensitive than a commercial magnetic bead-based method for the capture of target DNA from a pool of interfering genomic DNA.
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Affiliation(s)
- Kevin D Clark
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
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20
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Taskova M, Uhd J, Miotke L, Kubit M, Bell J, Ji HP, Astakhova K. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. Anal Chem 2017; 89:4363-4366. [PMID: 28382823 DOI: 10.1021/acs.analchem.7b00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New approaches for genomic DNA/RNA detection are in high demand in order to provide controls for existing enzymatic technologies and to create alternatives for emerging applications. In particular, there is an unmet need in rapid, reliable detection of short RNA regions which could open up new opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA followed by click assembly and analysis of the read sequence by various techniques. As we demonstrate in this paper, using our new approach, a viral RNA sequence can be detected in less than 2 h without the need for cDNA synthesis or any other enzymatic reactions and with a sensitivity of <10 pM target RNA.
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Affiliation(s)
- Maria Taskova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Uhd
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - Matthew Kubit
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - John Bell
- Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States.,Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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