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Journal articles on the topic 'Fluorogenic dyes'

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Author: Grafiati

Published: 22 June 2024

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1

Pham, Ha H., Christopher Szent-Gyorgyi, Wendy L. Brotherton, Brigitte F. Schmidt, Kimberly J. Zanotti, Alan S. Waggoner, and Bruce A. Armitage. "Bichromophoric dyes for wavelength shifting of dye-protein fluoromodules." Organic & Biomolecular Chemistry 13, no. 12 (2015): 3699–710. http://dx.doi.org/10.1039/c4ob02522a.

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2

Martin, Annabell, and Pablo Rivera Fuentes. "A Baldwin-favored Cyclization Inspires the Development of Fluorogenic Polymethine Dyes for Bioimaging." CHIMIA 78, no. 4 (April 24, 2024): 196–99. http://dx.doi.org/10.2533/chimia.2024.196.

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Fluorescence imaging is an invaluable tool to study biological processes, and fluorogenic dyes are crucial to enhance cell permeability and target intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and in vivo imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. Here, we present a general strategy to transform polymethine compounds into fluorogenic dyes by implementing a 5-exo-trig ring-closure. This method provides access to bright, fluorogenic polymethine dyes with emissions across the visible and near-infrared spectrum.

3

Mamaeva, Anastasiya A., Vladimir I. Martynov, Sergey M. Deyev, and Alexey A. Pakhomov. "Comparison of Colorimetric and Fluorometric Chemosensors for Protein Concentration Determination and Approaches for Estimation of Their Limits of Detection." Chemosensors 10, no. 12 (December 17, 2022): 542. http://dx.doi.org/10.3390/chemosensors10120542.

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Here, we present a direct comparison of different dyes and assays for the determination of protein concentrations. We compared the classical Bradford assay with two modern assays based on the fluorogenic dyes QuDye and ProteOrange and showed that the Bradford reagent achieved excellent results in the determination of protein concentrations as compared with more modern rivals. We also showed that standard approaches for determining the limit of detection (LoD) and limit of quantification (LoQ) may not work correctly with the tested dyes. We proposed a new approach that extends the standard algorithm for LoD and LoQ determination. This approach works well with both classical colorimetric and fluorogenic dyes, as well as with nontrivial fluorescent probes.

4

Krell, Katja, and Hans-Achim Wagenknecht. "Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry." Biomolecules 10, no. 3 (March 21, 2020): 480. http://dx.doi.org/10.3390/biom10030480.

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A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells.

5

Martin, Annabell, and Pablo Rivera-Fuentes. "Fluorogenic polymethine dyes by intramolecular cyclization." Current Opinion in Chemical Biology 80 (June 2024): 102444. http://dx.doi.org/10.1016/j.cbpa.2024.102444.

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6

Li, Chenge, Marie-Aude Plamont, Hanna L. Sladitschek, Vanessa Rodrigues, Isabelle Aujard, Pierre Neveu, Thomas Le Saux, Ludovic Jullien, and Arnaud Gautier. "Dynamic multicolor protein labeling in living cells." Chemical Science 8, no. 8 (2017): 5598–605. http://dx.doi.org/10.1039/c7sc01364g.

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7

Bruchez, Marcel P. "Dark dyes–bright complexes: fluorogenic protein labeling." Current Opinion in Chemical Biology 27 (August 2015): 18–23. http://dx.doi.org/10.1016/j.cbpa.2015.05.014.

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8

Qi, Jianjun, and Ching-Hsuan Tung. "Development of benzothiazole ‘click-on’ fluorogenic dyes." Bioorganic & Medicinal Chemistry Letters 21, no. 1 (January 2011): 320–23. http://dx.doi.org/10.1016/j.bmcl.2010.11.009.

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9

Gu, Lingyue, Kévin Renault, Anthony Romieu, Jean-Alexandre Richard, and Rajavel Srinivasan. "Synthesis and spectral properties of 6′-triazolyl-dihydroxanthene-hemicyanine fused near-infrared dyes." New Journal of Chemistry 44, no. 28 (2020): 12208–15. http://dx.doi.org/10.1039/d0nj01724h.

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10

Karpenko, Iuliia A., Yosuke Niko, Viktor P. Yakubovskyi, Andriy O. Gerasov, Dominique Bonnet, Yuriy P. Kovtun, and Andrey S. Klymchenko. "Push–pull dioxaborine as fluorescent molecular rotor: far-red fluorogenic probe for ligand–receptor interactions." Journal of Materials Chemistry C 4, no. 14 (2016): 3002–9. http://dx.doi.org/10.1039/c5tc03411f.

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Fluorescent solvatochromic dyes and molecular rotors have attracted considerable attention as fluorogenic probes because of background-free detection of biomolecules in live cells in no-wash conditions.

11

Wang, Xiaoqing, Qingsong Liu, Fen Qi, Lin Li, Hai-Dong Yu, Zhipeng Liu, and Wei Huang. "Benzothiazole–pyrimidine-based BODIPY analogues: promising luminophores with fluorescence sensing and imaging ability and asymmetrization-induced solid-state emission." Dalton Transactions 45, no. 43 (2016): 17274–80. http://dx.doi.org/10.1039/c6dt03469a.

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12

Kormos, Attila, Alexandra Egyed, Jasmine M. Olvany, Ágnes Szatmári, Adrienn Biró, Zsóka Csorba, Péter Kele, and Krisztina Németh. "A Bioorthogonal Double Fluorogenic Probe to Visualize Protein–DNA Interaction." Chemosensors 10, no. 1 (January 17, 2022): 37. http://dx.doi.org/10.3390/chemosensors10010037.

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Two sets of bioorthogonally applicable, double fluorogenic probes, capable of sensing DNA–protein interactions, were prepared by installing an azide or tetrazine motif onto structurally fluorogenic, DNA sensitive frames. Installation of these bioorthogonal functions onto DNA intercalating dyes furnished these scaffolds with reactivity based fluorogenicity, rendering these probes double-fluorogenic, AND-type logic switches that require the simultaneous occurrence of a bioorthogonal reaction and interaction with DNA to trigger high intensity fluorescence. The probes were evaluated for double fluorogenic behavior in the presence/absence of DNA and a complementary bioorthogonal function. Our studies revealed that azide and tetrazine appending thiazole orange frames show remarkable double fluorogenic features. One of these probes, a membrane permeable tetrazine modified thiazole orange derivative was further tested in live cell labeling studies. Cells expressing bioorthogonalized DNA-binding proteins showed intensive fluorescence characteristics of the localization of the proteins upon treatment with our double fluorogenic probe. On the contrary, labeling similarly bioorthogonalized cytosolic proteins did not result in the appearance of the fluorescence signal. These studies suggest that such double-fluorogenic probes are indeed capable of sensing DNA–protein interactions in cells.

13

Low, Michelle, Khin Yin Win, Enyi Ye, Shuhua Liu, Soon Huat Ng, Xiaoqun Zhou, and Ming-Yong Han. "Fluorogenic Quantification of Albumin." Australian Journal of Chemistry 67, no. 10 (2014): 1382. http://dx.doi.org/10.1071/ch14083.

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By optimising various fluorogenic dyes, non-fluorescent fluorescamine can react with primary amines to form highly fluorescent products, which is a simple, fast, and sensitive method for the quantification of albumin. The effects of pH, temperature, and chemicals were studied systematically to quantify albumin. The quantification method is more sensitive at alkaline pHs, affording measurement of proteins concentrations as low as 15 µg mL–1. Denaturation of albumin at elevated temperatures and/or use of chemicals, such as ethanol and acetone, can greatly improve the sensitivity of the albumin detection method. The simple, accurate, and reliable analysis of albumin contents under favourable conditions can be developed as an important method for early diagnosis of kidney disease.

14

Stensrud, Kenneth F., Kimberly J. Zanotti, Alan S. Waggoner, and Bruce A. Armitage. "Spectral Properties of Fluorogenic Thiophene-derived Triarylmethane Dyes." Photochemistry and Photobiology 95, no. 1 (November 23, 2018): 406–10. http://dx.doi.org/10.1111/php.13037.

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15

Liu, Pei, Vincent Grenier, Wootack Hong, Vikram R. Muller, and Evan W. Miller. "Fluorogenic Targeting of Voltage-Sensitive Dyes to Neurons." Journal of the American Chemical Society 139, no. 48 (November 20, 2017): 17334–40. http://dx.doi.org/10.1021/jacs.7b07047.

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16

Sokolov, A. I., A. A. Gorshkova, N. S. Baleeva, and M. S. Baranov. "Keto-Analogs of Arylidene-Imidazolones as Fluorogenic Dyes." Russian Journal of Bioorganic Chemistry 48, no. 6 (December 2022): 1367–71. http://dx.doi.org/10.1134/s1068162022060243.

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Abstract We report a series of (Z)-2-acetyl-4-benzyliden-1-methyl-1Н-imidazol-5(4Н)-ones with a pronounced solvent-dependent intensity of fluorescence variation. The introduction of the 2-acetyl group allows one to shift the absorption and emission maxima to the long-wavelength region. We have shown that these compounds can be used for staining the endoplasmic reticulum for fluorescent microscopy.

17

Bhasikuttan, Achikanath C., and Jyotirmayee Mohanty. "Targeting G-quadruplex structures with extrinsic fluorogenic dyes: promising fluorescence sensors." Chemical Communications 51, no. 36 (2015): 7581–97. http://dx.doi.org/10.1039/c4cc10030a.

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This article provides a brief account of the recent reports on the fluorescence properties of some of the fluorogenic dyes towards G-quadruplex DNAs, which have been turned into promising bio-analytical methods.

18

Vasilev, Aleksey A., Meglena I. Kandinska, Stanimir S. Stoyanov, Stanislava B. Yordanova, David Sucunza, Juan J. Vaquero, Obis D. Castaño, Stanislav Baluschev, and Silvia E. Angelova. "Halogen-containing thiazole orange analogues – new fluorogenic DNA stains." Beilstein Journal of Organic Chemistry 13 (December 28, 2017): 2902–14. http://dx.doi.org/10.3762/bjoc.13.283.

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Novel asymmetric monomeric monomethine cyanine dyes 5a–d, which are analogues of the commercial dsDNA fluorescence binder thiazole orange (TO), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields. Interactions of the new derivatives of TO with dsDNA have been investigated by absorption and fluorescence spectroscopy. The longest wavelength absorption bands in the UV–vis spectra of the target compounds are in the range of 509–519 nm and these are characterized by high molar absorptivities (63000–91480 L·mol−1·cm−1). All investigated dyes from the series are either not fluorescent or their fluorescence is quite low, but they become strongly fluorescent after binding to dsDNA. The influence of the substituents attached to the chromophores was investigated by combination of spectroscopic (UV–vis and fluorescence spectroscopy) and theoretical (DFT and TDDFT calculations) methods.

19

Dou, Wei-Tao, Ying Lv, Chunyan Tan, Guo-Rong Chen, and Xiao-Peng He. "Irreversible destruction of amyloid fibril plaques by conjugated polymer based fluorogenic nanogrenades." Journal of Materials Chemistry B 4, no. 26 (2016): 4502–6. http://dx.doi.org/10.1039/c6tb01351a.

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Supramolecular assembly between conjugated polymers and fluorescent dyes produces a unique class of fluorogenic “nanogrenades” with the ability to image as well as irreversibly destruct amyloid β fibril plaques by simple white-light irradiation.

20

Alfindee, Madher N., Yagya P. Subedi, Michelle M. Grilley, Jon Y. Takemoto, and Cheng-Wei T. Chang. "Antifungal Activities of 4″,6″-Disubstituted Amphiphilic Kanamycins." Molecules 24, no. 10 (May 16, 2019): 1882. http://dx.doi.org/10.3390/molecules24101882.

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Amphiphilic kanamycins derived from the classic antibiotic kanamycin have attracted interest due to their novel bioactivities beyond inhibition of bacteria. In this study, the recently described 4″,6″-diaryl amphiphilic kanamycins reported as inhibitors of connexin were examined for their antifungal activities. Nearly all 4″,6″-diaryl amphiphilic kanamycins tested had antifungal activities comparable to those of 4″,6″-dialkyl amphiphilic kanamycins, reported previously against several fungal strains. The minimal growth inhibitory concentrations (MICs) correlated with the degree of amphiphilicity (cLogD) of the di-substituted amphiphilic kanamycins. Using the fluorogenic dyes, SYTOXTM Green and propidium iodide, the most active compounds at the corresponding MICs or at 2×MICs caused biphasic dye fluorescence increases over time with intact cells. Further lowering the concentrations to half MICs caused first-order dye fluorescence increases. Interestingly, 4×MIC or 8×MIC levels resulted in fluorescence suppression that did not correlate with the MIC and plasma membrane permeabilization. The results show that 4″,6″-diaryl amphiphilic kanamycins are antifungal and that amphiphilicity parameter cLogD is useful for the design of the most membrane-active versions. A cautionary limitation of fluorescence suppression was revealed when using fluorogenic dyes to measure cell-permeation mechanisms with these antifungals at high concentrations. Finally, 4″,6″-diaryl amphiphilic kanamycins elevate the production of cellular reactive oxygen species as other reported amphiphilic kanamycins.

21

Diana, Rosita, Barbara Panunzi, Simona Concilio, Francesco Marrafino, Rafi Shikler, Tonino Caruso, and Ugo Caruso. "The Effect of Bulky Substituents on Two π-Conjugated Mesogenic Fluorophores. Their Organic Polymers and Zinc-Bridged Luminescent Networks." Polymers 11, no. 9 (August 22, 2019): 1379. http://dx.doi.org/10.3390/polym11091379.

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From a dicyano-phenylenevinylene (PV) and an azobenzene (AB) skeleton, two new symmetrical salen dyes were obtained. Terminal bulky substituents able to reduce intermolecular interactions and flexible tails to guarantee solubility were added to the fluorogenic cores. Photochemical performances were investigated on the small molecules in solution, as neat crystals and as dopants in polymeric matrixes. High fluorescence quantum yield in the orange-red region was observed for the brightest emissive films (88% yield). The spectra of absorption and fluorescence were predicted by Density Functional Theory (DFT) calculations. The predicted energy levels of the frontier orbitals are in good agreement with voltammetry and molecular spectroscopy measures. Employing the two dyes as dopants of a nematic polymer led to remarkable orange or yellow luminescence, which dramatically decreases in on-off switch mode after liquid crystal (LC) order was lost. The fluorogenic cores were also embedded in organic polymers and self-assembly zinc coordination networks to transfer the emission properties to a macro-system. The final polymers emit from red to yellow both in solution and in the solid state and their photoluminescence (PL) performance are, in some cases, enhanced when compared to the fluorogenic cores.

22

Smith, H. V., A. M. Grimason, C. Benton, and J. F. W. Parker. "The Occurrence of Cryptosporidium Spp. Oocysts in Scottish Waters, and the Development of a Fluorogenic Viability Assay for Individual Cryptosporidium spp. Oocysts." Water Science and Technology 24, no. 2 (July 1, 1991): 169–72. http://dx.doi.org/10.2166/wst.1991.0051.

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A total of 262 water-related samples were analysed for the presence of Cryptosporidium spp. oocysts, of which 39.3% were positive, over a twelve month period. Similar data were obtained for their occurrence in samples of both raw and treated water from Scotland, with 40.5% of raw water and 40.1% of treated water being positive. Fewer oocysts were detected in the summer than in the autumn, winter or spring. In a 12 month survey of water used for abstraction, oocysts were detected at various times throughout the year in both raw and treated water. A series of conventional and fluorogenic dyes was used, in conjunction with a fluorescent labelled monoclonal antibody, in an attempt to assess their potential fox imprpving the identification of oocysts in water-related samples. In addition, preliminary data regarding the possible use of fluorogenic vital dyes as indicators of in vitro excystation and viability are presented.

23

Silva, Gloria L., Volkan Ediz, David Yaron, and Bruce A. Armitage. "Experimental and Computational Investigation of Unsymmetrical Cyanine Dyes: Understanding Torsionally Responsive Fluorogenic Dyes." Journal of the American Chemical Society 129, no. 17 (May 2007): 5710–18. http://dx.doi.org/10.1021/ja070025z.

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24

Qi, Jianjun, Myung-Shin Han, Yu-Cheng Chang, and Ching-Hsuan Tung. "Developing Visible Fluorogenic ‘Click-On’ Dyes for Cellular Imaging." Bioconjugate Chemistry 22, no. 9 (September 21, 2011): 1758–62. http://dx.doi.org/10.1021/bc200282t.

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25

Kisin-Finfer, Einat, and Doron Shabat. "New repertoire of ‘donor-two-acceptor’ NIR fluorogenic dyes." Bioorganic & Medicinal Chemistry 21, no. 12 (June 2013): 3602–8. http://dx.doi.org/10.1016/j.bmc.2013.02.049.

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26

Qi, Jianjun, and Ching-Hsuan Tung. "ChemInform Abstract: Development of Benzothiazole “Click-On” Fluorogenic Dyes." ChemInform 42, no. 20 (April 21, 2011): no. http://dx.doi.org/10.1002/chin.201120179.

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27

Vincent, Steve, Suman Mallick, Guillaume Barnoin, Hoang-Ngoan Le, Benoît Y. Michel, and Alain Burger. "An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection." Molecules 27, no. 7 (March 31, 2022): 2267. http://dx.doi.org/10.3390/molecules27072267.

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The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of this task, as they do not exhibit good brightness in aqueous buffer media, develop aggregation and/or are not easily conjugated to oligodeoxynucleotides (ODNs) while keeping their photophysics intact. Herein, an important modification strategy was employed for a well-known fluorophore, 2-(4-(diethylamino)phenyl)-3-hydroxychromone (dEAF). Although this push–pull dye absorbs intensively in the visible range and shows emission with large Stokes shifts in all organic solvents, it is strongly quenched in water. This Achilles’ heel prompted us to implement a new strategy to obtain a series of dyes that retain all the photophysical features of dEAF in water, conjugate readily with oligonucleotides, and furthermore demonstrate sensitivity to hydration, thus paving the way for a high-performance fluorogenic DNA hybridization probe.

28

Yan, Qi, Brigitte F. Schmidt, Lydia A. Perkins, Matharishwan Naganbabu, Saumya Saurabh, Susan K. Andreko, and Marcel P. Bruchez. "Near-instant surface-selective fluorogenic protein quantification using sulfonated triarylmethane dyes and fluorogen activating proteins." Organic & Biomolecular Chemistry 13, no. 7 (2015): 2078–86. http://dx.doi.org/10.1039/c4ob02309a.

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29

Debieu, Sylvain, and Anthony Romieu. "In situ formation of pyronin dyes for fluorescence protease sensing." Organic & Biomolecular Chemistry 15, no. 12 (2017): 2575–84. http://dx.doi.org/10.1039/c7ob00370f.

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A cutting-edge strategy for fluorogenic sensing of proteases (leucine aminopeptidase for the proof of concept) and based on the “covalent-assembly” principle is reported. Non-fluorescent mixed bis-aryl ethers are readily converted into a fluorescent pyronin through a domino process triggered by the peptide bond cleavage event caused by the targeted enzyme.

30

Chi, Weijie, Lu Huang, Chao Wang, Davin Tan, Zhaochao Xu, and Xiaogang Liu. "A unified fluorescence quenching mechanism of tetrazine-based fluorogenic dyes: energy transfer to a dark state." Materials Chemistry Frontiers 5, no. 18 (2021): 7012–21. http://dx.doi.org/10.1039/d1qm00852h.

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31

Ilieva, Sonia, Nadezhda Bozova, Miroslav Rangelov, Nadezhda Todorova, Aleksey Vasilev, and Diana Cheshmedzhieva. "Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay." Molecules 29, no. 1 (December 23, 2023): 114. http://dx.doi.org/10.3390/molecules29010114.

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A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra. The applicability of the dyes as fluorogenic nucleic acid probes has been proven by fluorescence titration, and their binding constants have been calculated. The mode of ligand–dsDNA/RNA interaction was rationalized by means of CD spectroscopy, molecular docking analysis, and fluorescent intercalator displacement experiments.

32

Constantin, Tudor P., Gloria L. Silva, Kelly L. Robertson, Tamara P. Hamilton, Kaitlin Fague, Alan S. Waggoner, and Bruce A. Armitage. "Synthesis of New Fluorogenic Cyanine Dyes and Incorporation into RNA Fluoromodules." Organic Letters 10, no. 8 (April 2008): 1561–64. http://dx.doi.org/10.1021/ol702920e.

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33

Chauhan, Dinesh Pratapsinh, Tanmoy Saha, Mayurika Lahiri, and Pinaki Talukdar. "BODIPY based ‘click on’ fluorogenic dyes: application in live cell imaging." Tetrahedron Letters 55, no. 1 (January 2014): 244–47. http://dx.doi.org/10.1016/j.tetlet.2013.11.003.

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34

O’Connor, Liam J., Ishna N. Mistry, Sarah L. Collins, Lisa K. Folkes, Graham Brown, Stuart J. Conway, and Ester M. Hammond. "CYP450 Enzymes Effect Oxygen-Dependent Reduction of Azide-Based Fluorogenic Dyes." ACS Central Science 3, no. 1 (December 19, 2016): 20–30. http://dx.doi.org/10.1021/acscentsci.6b00276.

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35

Zhang, Yuanwei, Xiling Yue, Bosung Kim, Sheng Yao, Mykhailo V. Bondar, and Kevin D. Belfield. "Bovine Serum Albumin Nanoparticles with Fluorogenic Near-IR-Emitting Squaraine Dyes." ACS Applied Materials & Interfaces 5, no. 17 (August 30, 2013): 8710–17. http://dx.doi.org/10.1021/am402361w.

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36

Ho, Nan-hui, Ralph Weissleder, and Ching-Hsuan Tung. "Development of water-soluble far-red fluorogenic dyes for enzyme sensing." Tetrahedron 62, no. 4 (January 2006): 578–85. http://dx.doi.org/10.1016/j.tet.2005.10.020.

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37

NISHIZAWA, Seiichi, Yukina YOSHINO, Mengmeng HE, Kei HIGUCHI, Nao TOGASHI, Michiyuki SUZUKI, Yugo IGARASHI, and Yusuke SATO. "Fluorogenic Monomethine Cyanine Dyes for Nucleolar RNA Imaging in Living Cells." BUNSEKI KAGAKU 73, no. 3 (March 5, 2024): 79–86. http://dx.doi.org/10.2116/bunsekikagaku.73.79.

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38

Choi, Sang-Kee, Jonghoon Kim, and Eunha Kim. "Overview of Syntheses and Molecular-Design Strategies for Tetrazine-Based Fluorogenic Probes." Molecules 26, no. 7 (March 26, 2021): 1868. http://dx.doi.org/10.3390/molecules26071868.

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Various bioorthogonal chemistries have been used for fluorescent imaging owing to the advantageous reactions they employ. Recent advances in bioorthogonal chemistry have revolutionized labeling strategies for fluorescence imaging, with inverse electron demand Diels–Alder (iEDDA) reactions in particular attracting recent attention owing to their fast kinetics and excellent specificity. One of the most interesting features of the iEDDA labeling strategy is that tetrazine-functionalized dyes are known to act as fluorogenic probes. In this review, we will focus on the synthesis, molecular-design strategies, and bioimaging applications of tetrazine-functionalized fluorogenic probes. Traditional Pinner reaction and “Pinner-like” reactions for tetrazine synthesis are discussed here, as well as metal-catalyzed C–C bond formations with convenient tetrazine intermediates and the fabrication of tetrazine-conjugated fluorophores. In addition, four different quenching mechanisms for tetrazine-modified fluorophores are presented.

39

Zanotti, Kimberly J., Gloria L. Silva, Yehuda Creeger, Kelly L. Robertson, Alan S. Waggoner, Peter B. Berget, and Bruce A. Armitage. "Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments." Org. Biomol. Chem. 9, no. 4 (2011): 1012–20. http://dx.doi.org/10.1039/c0ob00444h.

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40

Demeter, Orsolya, Attila Kormos, Christine Koehler, Gábor Mező, Krisztina Németh, Eszter Kozma, Levente B. Takács, Edward A. Lemke, and Péter Kele. "Bisazide Cyanine Dyes as Fluorogenic Probes for Bis-Cyclooctynylated Peptide Tags and as Fluorogenic Cross-Linkers of Cyclooctynylated Proteins." Bioconjugate Chemistry 28, no. 5 (April 28, 2017): 1552–59. http://dx.doi.org/10.1021/acs.bioconjchem.7b00178.

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41

Bozhanova, Nina, Mikhail Baranov, Nadezhda Baleeva, Alexey Gavrikov, and Alexander Mishin. "Red-Shifted Aminated Derivatives of GFP Chromophore for Live-Cell Protein Labeling with Lipocalins." International Journal of Molecular Sciences 19, no. 12 (November 28, 2018): 3778. http://dx.doi.org/10.3390/ijms19123778.

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Fluorogens are an attractive type of dye for imaging applications, eliminating time-consuming washout steps from staining protocols. With just a handful of reported fluorogen-protein pairs, mostly in the green region of spectra, there is a need for the expansion of their spectral range. Still, the origins of solvatochromic and fluorogenic properties of the chromophores suitable for live-cell imaging are poorly understood. Here we report on the synthesis and labeling applications of novel red-shifted fluorogenic cell-permeable green fluorescent protein (GFP) chromophore analogs.

42

Patalag, Lukas J., and Daniel B. Werz. "Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts." Beilstein Journal of Organic Chemistry 12 (December 14, 2016): 2739–47. http://dx.doi.org/10.3762/bjoc.12.270.

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Abstract:

Herein, we report on the synthesis and characterization of novel fluorescent fatty acids with large Stokes shifts. Three examples consisting of the same number of carbon atoms and thus of similar chain length are presented differing in their degree of unsaturation. As major fluorogenic contributor at the terminus benzo[c][1,2,5]thiadiazole was used. Respective syntheses based on Wittig reactions followed by iodine-mediated isomerization are presented. The absorption properties are modulated by the number of conjugated C=C double bonds of the oligoene chain ranging from one to three. Large Stokes shifts of about 4900–5700 cm−1 and fluorescence quantum yields of up to 0.44 were observed.

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Hannig, Christian, Marie Follo, Elmar Hellwig, and Ali Al-Ahmad. "Visualization of adherent micro-organisms using different techniques." Journal of Medical Microbiology 59, no. 1 (January 1, 2010): 1–7. http://dx.doi.org/10.1099/jmm.0.015420-0.

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The visualization and quantification of adherent bacteria is still one of the most relevant topics in microbiology. Besides electron microscopic techniques such as transmission electron microscopy, scanning electron microscopy and environmental scanning electron microscopy, modern fluorescence microscopic approaches based on fluorogenic dyes offer detailed insight into bacterial biofilms. The aim of the present review was to provide an overview of the advantages and disadvantages of different methods for visualization of adherent bacteria with a special focus on the experiences gained in dental research.

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Ediz, Volkan, Jihoon L. Lee, Bruce A. Armitage, and David Yaron. "Molecular Engineering of Torsional Potentials in Fluorogenic Dyes via Electronic Substituent Effects." Journal of Physical Chemistry A 112, no. 40 (October 9, 2008): 9692–701. http://dx.doi.org/10.1021/jp805546s.

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Klymchenko, Andrey S. "Solvatochromic and Fluorogenic Dyes as Environment-Sensitive Probes: Design and Biological Applications." Accounts of Chemical Research 50, no. 2 (January 9, 2017): 366–75. http://dx.doi.org/10.1021/acs.accounts.6b00517.

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Chen, Lei, Fei Li, Mitoshi Nandi, Lu Huang, Zhizhong Chen, Junfa Wei, Weijie Chi, Xiaogang Liu, and Jun Yang. "Towards tetrazine-based near-infrared fluorogenic dyes: Is there a wavelength limit?" Dyes and Pigments 177 (June 2020): 108313. http://dx.doi.org/10.1016/j.dyepig.2020.108313.

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Collot, Mayeul, Rémy Kreder, Anatoliy L. Tatarets, Leonid D. Patsenker, Yves Mely, and Andrey S. Klymchenko. "Bright fluorogenic squaraines with tuned cell entry for selective imaging of plasma membrane vs. endoplasmic reticulum." Chemical Communications 51, no. 96 (2015): 17136–39. http://dx.doi.org/10.1039/c5cc06094j.

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Ta, Daniel D., and Sergei V. Dzyuba. "Squaraine-Based Optical Sensors: Designer Toolbox for Exploring Ionic and Molecular Recognitions." Chemosensors 9, no. 11 (October 25, 2021): 302. http://dx.doi.org/10.3390/chemosensors9110302.

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Abstract:

Small molecule-based chromogenic and fluorogenic probes play an indispensable role in many sensing applications. Ideal optical chemosensors should provide selectivity and sensitivity towards a variety of analytes. Synthetic accessibility and attractive photophysical properties have made squaraine dyes an enticing platform for the development of chemosensors. This review highlights the versatility of modular assemblies of squaraine-based chemosensors and chemodosimeters that take advantage of the availability of various structurally and functionally diverse recognition motifs, as well as utilizing additional recognition capabilities due to the unique structural features of the squaraine ring.

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Ryazantsev, Dmitry Y., Maksim V. Kvach, Dmitry A. Tsybulsky, Igor A. Prokhorenko, Irina A. Stepanova, Yury V. Martynenko, Sergey V. Gontarev, Vadim V. Shmanai, Sergey K. Zavriev, and Vladimir A. Korshun. "Design of molecular beacons: 3′ couple quenchers improve fluorogenic properties of a probe in real-time PCR assay." Analyst 139, no. 11 (2014): 2867–72. http://dx.doi.org/10.1039/c4an00081a.

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Muñoz Resta, Ignacio, and Francisco Galindo. "Phenol-based styrylpyrylium dyes for trace water detection via chromogenic and fluorogenic responses." Dyes and Pigments 197 (January 2022): 109908. http://dx.doi.org/10.1016/j.dyepig.2021.109908.

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