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Maddeshiya T, Jaiswal MK, Tamrakar A, Mishra G, Awasthi C, Pandey MD. Pyrene Appendant Triazole-based Chemosensors for Sensing Applications. Curr Org Synth 2024; 21:421-435. [PMID: 37345247 DOI: 10.2174/1570179420666230621124119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 06/23/2023]
Abstract
Over the last two decades, the design and development of fluorescent chemosensors for the targeted detection of Heavy Transition-metal (HTM) ions, anions, and biological analytes, have drawn much interest. Since the introduction of click chemistry in 2001, triazole moieties have become an increasingly prominent theme in chemosensors. Triazoles generated via click reactions are crucial for sensing various ions and biological analytes. Recently, the number of studies in the field of pyrene appendant triazole moieties has risen dramatically, with more sophisticated and reliable triazole-containing chemosensors for various analytes of interest described. This tutorial review provides a general overview of pyrene appendant-triazole-based chemosensors that can detect a variety of metal cations, anions, and neutral analytes by using modular click-derived triazoles.
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Affiliation(s)
- Tarkeshwar Maddeshiya
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Arpna Tamrakar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Gargi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Chhama Awasthi
- Department of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi, 110016, India
| | - Mrituanjay D Pandey
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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Zheng K, Ye Y, Shi Y, Xu Y, Yang Z, Ma P, Wang J, Niu J. dl-Serine Covalently Ornamented and Ln 3+-Incorporated Arsenotungstates with Fast-Responsive Photochromic and Photoinduced Luminescent Switchable Behaviors. Inorg Chem 2022; 61:15871-15879. [PMID: 36174202 DOI: 10.1021/acs.inorgchem.2c01806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three isostructural dl-serine covalently functionalized and multinuclear lanthanide (Ln3+)-embedded arsenotungstates, K2[{As4W44O137(OH)18(H2O)2(dl-Ser)2}{Ln2(H2O)4(dl-Ser)}2{Ln(H2O)7}2]·70H2O (Ln = Sm (1), Eu (2), and Gd (3); dl-Ser = C3H7NO3), were prepared, where the centrosymmetric [{As4W44O137(OH)18(H2O)2(dl-Ser)2}{Ln2(H2O)4(dl-Ser)}2]8- polyanion consists of two {As2W19O59(OH)8(H2O)}6- fragments, integrated with a two-dl-serine-ornamented [W6O23(OH)2(dl-Ser)2{Ln2(H2O)4}2]8- segment. In addition, the photochromic transformation of solid-state compounds 1-3 was observed from colorless to blue after a UV illumination of 4 min, and the decay process lasted as long as ∼20 h in the dark. The coloration kinetic half-life (t1/2) values of compounds 1, 2, and 3 were calculated to be 0.597, 0.920, and 0.723 min, respectively. Furthermore, the luminescent properties and energy migration from arsenotungstates and organic chromophores to Sm3+ and Eu3+ ions in 1 and 2 have been intensively investigated. Further analysis manifests that 1 possesses an effective luminescent switchable behavior, triggered by its fast-responsive photochromism effect.
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Affiliation(s)
- Kangting Zheng
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Yajing Ye
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Yanan Shi
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Yaxuan Xu
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Ziyu Yang
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Pengtao Ma
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Jingping Wang
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Jingyang Niu
- Henan Key Laboratory of Polyoxometalate Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
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Zhao X, Zhao L, Xiao Q, Xiong H. Intermolecular hydrogen-bond interaction to promote thermoreversible 2'-deoxyuridine-based AIE-organogels. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Criado-Gonzalez M, Fores JR, Carvalho A, Blanck C, Schmutz M, Kocgozlu L, Schaaf P, Jierry L, Boulmedais F. Phase Separation in Supramolecular Hydrogels Based on Peptide Self-Assembly from Enzyme-Coated Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10838-10845. [PMID: 31334660 DOI: 10.1021/acs.langmuir.9b01420] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spatial localization of biocatalysts, such as enzymes, has recently proven to be an effective process to direct supramolecular self-assemblies in a spatiotemporal way. In this work, silica nanoparticles (NPs) functionalized covalently by alkaline phosphatase (NPs@AP) induce the localized growth of self-assembled peptide nanofibers from NPs by dephosphorylation of Fmoc-FFpY peptides (Fmoc: fluorenylmethyloxycarbonyl; F: phenylalanine; Y: tyrosine; p: phosphate group). The fibrillary nanoarchitecture around NPs@AP underpins a homogeneous hydrogel, which unexpectedly undergoes a macroscopic shape change over time. This macroscopic change is due to a phase separation leading to a dense phase (in NPs and nanofibers) in the center of the vial and surrounded by a dilute one, which still contains NPs and peptide self-assemblies. We thus hypothesize that the phase separation is not a syneresis process. Such a change is only observed when the enzymes are localized on the NPs. The dense phase contracts with time until reaching a constant volume after several days. For a given phosphorylated peptide concentration, the dense phase contracts faster when the NPs@AP concentration is increased. For a given NPs@AP concentration, it condenses faster when the peptide concentration increases. We hypothesize that the appearance of a dense phase is not only due to attractive interactions between NPs@AP but also to the strong interactions of self-assembled peptide nanofibers with the enzymes, covalently fixed on the NPs.
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Affiliation(s)
- Miryam Criado-Gonzalez
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Jennifer Rodon Fores
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Alain Carvalho
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Christian Blanck
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Marc Schmutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Leyla Kocgozlu
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Pierre Schaaf
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
- Institut National de la Santé et de la Recherche Médicale, UMR-S 1121, "Biomatériaux et Bioingénierie" , 67087 Strasbourg , France
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Fédération de Médecine Translationnelle de Strasbourg and Fédération des Matériaux et Nanoscience d'Alsace , 67000 Strasbourg , France
| | - Loïc Jierry
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
| | - Fouzia Boulmedais
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR 22 , 67034 Strasbourg , France
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Ratajczak T, Uszczyńska B, Frydrych-Tomczak E, Chmielewski MK. The "Clickable" Method for Oligonucleotide Immobilization Onto Azide-Functionalized Microarrays. Methods Mol Biol 2016; 1368:25-36. [PMID: 26614066 DOI: 10.1007/978-1-4939-3136-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The DNA microarray technique was supposed to help identifying and analyzing the expression level of tens of thousands of genes in the whole genome. But there is a serious problem concerning fabrication of the microarrays by chemical synthesis, such as specific and efficient linking of probes to a solid support. Therefore, we reckon that applying "click" chemistry to covalently anchor oligonucleotides on chemically modified supports may help construct microarrays in applications such as gene identification. Silanization of the glass support with organofunctional silane makes it possible to link azide groups on glass surface and the nucleic acid probe that is equipped with a pentynyl group. This is followed by direct spotting of the nucleic acid on the azide-modified glass support in the presence of copper ions, and this is a frequently applied method of "click" chemistry.
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Affiliation(s)
- Tomasz Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Barbara Uszczyńska
- Centre for Genomic Regulation (CGR), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Emilia Frydrych-Tomczak
- Poznan Science and Technology Park, Adam Mickiewicz University Foundation, Rubiez 46, 61-612, Poznan, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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Kath-Schorr S. Cycloadditions for Studying Nucleic Acids. Top Curr Chem (Cham) 2015; 374:4. [PMID: 27572987 DOI: 10.1007/s41061-015-0004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.
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Affiliation(s)
- Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, University of Bonn, Bonn, Germany.
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Gao W, Zheng D, Dong Z, Wu L, Bi L. Preparation of green luminescence composite film and study of electrofluorochromic performance. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.07.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Sawant AA, Tanpure AA, Mukherjee PP, Athavale S, Kelkar A, Galande S, Srivatsan SG. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucleic Acids Res 2015; 44:e16. [PMID: 26384420 PMCID: PMC4737177 DOI: 10.1093/nar/gkv903] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 08/31/2015] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Progya P Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Soumitra Athavale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ashwin Kelkar
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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Olive AGL, Abdullah NH, Ziemecka I, Mendes E, Eelkema R, van Esch JH. Spatial and Directional Control over Self-Assembly Using Catalytic Micropatterned Surfaces. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310776] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Olive AGL, Abdullah NH, Ziemecka I, Mendes E, Eelkema R, van Esch JH. Spatial and directional control over self-assembly using catalytic micropatterned surfaces. Angew Chem Int Ed Engl 2014; 53:4132-6. [PMID: 24615796 DOI: 10.1002/anie.201310776] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Indexed: 01/03/2023]
Abstract
Catalyst-assisted self-assembly is widespread in nature to achieve spatial control over structure formation. Reported herein is the formation of hydrogel micropatterns on catalytic surfaces. Gelator precursors react on catalytic sites to form building blocks which can self-assemble into nanofibers. The resulting structures preferentially grow where the catalyst is present. Not only is a first level of organization, allowing the construction of hydrogel micropatterns, achieved but a second level of organization is observed among fibers. Indeed, fibers grow with their main axis perpendicular to the substrate. This feature is directly linked to a unique mechanism of fiber formation for a synthetic system. Building blocks are added to fibers in a confined space at the solid-liquid interface.
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Affiliation(s)
- Alexandre G L Olive
- Advanced Soft Matter Group, Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL Delft (The Netherlands)
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Qing G, Shan X, Chen W, Lv Z, Xiong P, Sun T. Solvent-Driven Chiral-Interaction Reversion for Organogel Formation. Angew Chem Int Ed Engl 2014; 53:2124-9. [DOI: 10.1002/anie.201308554] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/17/2013] [Indexed: 12/22/2022]
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Xie L, Zheng H, Ye W, Qiu S, Lin Z, Guo L, Qiu B, Chen G. Novel colorimetric molecular switch based on copper(I)-catalyzed azide-alkyne cycloaddition reaction and its application for flumioxazin detection. Analyst 2014. [PMID: 23188065 DOI: 10.1039/c2an36023c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel colorimetric switch based on the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction has been developed. G-quadruplex-hemin DNAzyme catalyzes the oxidation of 2,2'-azinobis(3-ethylbenzothiozoline)-6-sulfonic acid (ABTS) to form ABTS˙(+), the UV absorbance of the solution increased greatly and the color of the solution changed to dark green. However, in the presence of an azide complex, the absorbance signal decreased and the solution became light green since the catalytic ability of the hemin was inhibited by the azide groups. However, once propargylamine has been added into the above reaction system, which would react with azide groups through the CuAAC reaction, the solution becomes dark green again and the absorption intensity of the system is also increased. The proposed switch allows a good reversibility and can be identified clearly by the naked eye. In addition, the method has been applied to detect some pesticides, which have alkynyl groups (flumioxazin), with high sensitivity and selectivity, where the UV absorbance has a direct linear relationship with the logarithm of flumioxazin concentrations in the range of 0.14-14 nM, and the limit of detection was 0.056 nM (S/N = 3), which can meet the requirement of the maximum residue limits (MRLs) of United States of America (56 nM).
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Affiliation(s)
- Lidan Xie
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China
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Pearson HA, Urban MW. Simple click reactions on polymer surfaces leading to antimicrobial behavior. J Mater Chem B 2014; 2:2084-2087. [DOI: 10.1039/c3tb21865a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microwave plasma and click chemistry on polymeric substrates.
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Affiliation(s)
- Heather A. Pearson
- Department of Materials Science and Engineering
- Center for Optical Materials Sciences and Engineering Technologies (COMSET)
- Clemson University
- Clemson, USA
| | - Marek W. Urban
- Department of Materials Science and Engineering
- Center for Optical Materials Sciences and Engineering Technologies (COMSET)
- Clemson University
- Clemson, USA
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Azam MS, Gibbs-Davis JM. Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy. Anal Chem 2013; 85:8031-8. [DOI: 10.1021/ac401009u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Md. Shafiul Azam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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Hashidzume A, Nakamura T, Sato T. Copper-catalyzed azide-alkyne cycloaddition oligomerization of 3-azido-1-propyne derivatives. POLYMER 2013. [DOI: 10.1016/j.polymer.2013.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Mei H, Budow S, Seela F. Construction and assembly of chimeric DNA: oligonucleotide hybrid molecules composed of parallel or antiparallel duplexes and tetrameric i-motifs. Biomacromolecules 2012; 13:4196-204. [PMID: 23121010 DOI: 10.1021/bm301471d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chimeric DNA containing parallel (ps) and antiparallel (aps) duplex elements as well as poly-dC tracts were designed and synthesized. Oligonucleotide duplexes with ps chain orientation containing reverse Watson-Crick dA-dT base pairs and short d(C)2 tails are stabilized under slightly acidic conditions by hemiprotonated dCH+-dC base pairs ("clamp" effect). Corresponding molecules with aps orientation containing Watson-Crick dA-dT base pairs do not show this phenomenon. Chimeric DNA with ps duplex elements and long d(C)5 tails at one or at both ends assemble to tetrameric i-motif structures. Molecules with two terminal d(C)5 tails form multimeric assemblies which have the potential to form nanoscopic scaffolds. A preorganization of the ps duplex chains stabilizes the i-motif assemblies up to almost neutral conditions as evidenced by thermal melting and gel electrophoresis. Although, ps DNA is generally less stable than aps DNA, the aps duplexes contribute less to the stability of the i-motif than ps DNA.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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Ingale SA, Seela F. A ratiometric fluorescent on-off Zn2+ chemosensor based on a tripropargylamine pyrene azide click adduct. J Org Chem 2012; 77:9352-6. [PMID: 23030804 DOI: 10.1021/jo3014319] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new, easy-to-prepare and highly selective pyrene-linked tris-triazole amine fluorescent chemosensor has been designed from tripropargylamine and pyrene azide using Cu(I)-catalyzed click chemistry. The fluorescence on-off sensor 1 is highly selective for Zn(2+) displaying a ratiometric change in emission. The relative intensity ratio of monomer to excimer fluorescence (M(376)/E(465)) of the sensor increases 80-fold upon the addition of 10 equiv of Zn(2+) ions (with a detection limit of 0.2 μM).
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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Such GK, Johnston AP, Liang K, Caruso F. Synthesis and functionalization of nanoengineered materials using click chemistry. Prog Polym Sci 2012. [DOI: 10.1016/j.progpolymsci.2011.12.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Xiong H, Leonard P, Seela F. Construction and assembly of branched Y-shaped DNA: "click" chemistry performed on dendronized 8-aza-7-deazaguanine oligonucleotides. Bioconjug Chem 2012; 23:856-70. [PMID: 22443223 DOI: 10.1021/bc300013k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Branched DNA was synthesized from tripropargylated oligonucleotides by the Huisgen-Meldal-Sharpless cycloaddition using "stepwise and double click" chemistry. Dendronized oligonucleotides decorated with 7-tripropargylamine side chains carrying two terminal triple bonds were further functionalized with bis-azides to give derivatives with two terminal azido groups. Then, the branched side chains with two azido groups or two triple bonds were combined with DNA-fragments providing the corresponding clickable function. Both concepts afforded branched (Y-shaped) three-armed DNA. Annealing of branched DNA with complementary oligonucleotides yielded supramolecular assemblies. The concept of "stepwise and double click" chemistry combined with selective hybridization represents a flexible tool to generate DNA nanostructures useful for various purposes in DNA diagnostics, delivery, and material science applications.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Uszczyńska B, Ratajczak T, Frydrych E, Maciejewski H, Figlerowicz M, Markiewicz WT, Chmielewski MK. Application of click chemistry to the production of DNA microarrays. LAB ON A CHIP 2012; 12:1151-1156. [PMID: 22318451 DOI: 10.1039/c2lc21096g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction was applied as the novel method of DNA immobilization on a modified solid support. The CuAAC click reaction enables the covalent binding of DNA modified with pentynyl groups at its 5'-end to azide-loaded slides. Click microarrays were produced using this approach and successfully employed in biological/model experiments.
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Affiliation(s)
- Barbara Uszczyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Ramanathan M, Kilbey, II SM, Ji Q, Hill JP, Ariga K. Materials self-assembly and fabrication in confined spaces. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16629a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Xiong H, Seela F. Stepwise "click" chemistry for the template independent construction of a broad variety of cross-linked oligonucleotides: influence of linker length, position, and linking number on DNA duplex stability. J Org Chem 2011; 76:5584-97. [PMID: 21591729 DOI: 10.1021/jo2004988] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Münster, Germany
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