Relevant bibliographies by topics / Fluorescent Dye Molecules

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Academic literature on the topic 'Fluorescent Dye Molecules'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Fluorescent Dye Molecules"

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Windsor, S. A., N. J. Harrison, and M. H. Tinker. "Electro-fluorescence studies of the binding of fluorescent dyes to sepiolite." Clay Minerals 31, no. 1 (March 1996): 81–94. http://dx.doi.org/10.1180/claymin.1996.031.1.08.

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AbstractAqueous suspensions of sepiolite, tagged with fluorescent dyes, have been studied using electro-fluorescence polarization spectroscopy. The binding modes of some 37 fluorescent dyes and optical brightening agents to the rod-like sepiolite particles have been determined. Many of the dyes are found to bind with a degree of order to the clay particle's major axis. The binding geometries of the cationic dye molecules tested were found to be dependent upon molecular size. This supports the view that these cationic dye molecules are constrained within the channels which are characteristic of the mineral sepiolite. Results for uncharged and anionic dye molecules are also presented; no dependence of binding geometry upon molecular size was found. The anionic molecules are most likely to associate with the exterior cationic magnesium surface. The results indicate that some of the anionic dyes are too large to fit in the channels. Some of the uncharged molecules adopt a number of orientations upon binding which gives rise to an average geometry being observed for these dyes.
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Collings, David A. "Anthocyanin in the Vacuole of Red Onion Epidermal Cells Quenches Other Fluorescent Molecules." Plants 8, no. 12 (December 12, 2019): 596. http://dx.doi.org/10.3390/plants8120596.

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Peels from the inner epidermis of onion bulbs are a model system in plant cell biology. While the inner epidermis of red onions is characteristically white, small patches of cells sometimes redden, containing vacuolar anthocyanin. This study investigated the spectroscopic properties of these anthocyanic cells. When fluorescent dyes were loaded into the vacuole of onion epidermal cells, the anthocyanic cells showed decreased dye fluorescence. This decrease was observed for fluorescein and carboxyfluorescein that are pumped into the vacuole by anion transporters, for acridine orange which acid loads into the vacuole, and for the fluorescent sugar analogue esculin loaded into the vacuole by sucrose transporters. Similar decreases in carboxyfluorescein fluorescence were observed when dye was loaded into the vacuoles of several other plant species, but decreases were not observed for dyes resident in the tonoplast membrane. As cellular physiology was unaffected in the anthocyanic cells, with cytoplasmic streaming, vacuolar and cytoplasmic pH not being altered, the decreased dye fluorescence from the anthocyanic cells can be attributed to fluorescence quenching. Furthermore, because quenching decreased with increasing temperature. It was concluded, therefore, that vacuolar anthocyanin can statically quench other fluorescent molecules in vivo, an effect previously demonstrated for anthocyanin in vitro.
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Wu, Jian, Yongjun Du, Chunyan Wang, and Tao Chen. "The Detection of a Fluorescent Dye by Surface-Enhanced Fluorescence with the Addition of Silver Nanoparticles and Its Application for the Space Station." Journal of Nanoscience and Nanotechnology 20, no. 5 (May 1, 2020): 3195–200. http://dx.doi.org/10.1166/jnn.2020.17383.

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Surface-enhanced fluorescence detection has large potential for detecting many chemical and biological trace analytes. This paper presents a novel method for preparing silver nanomaterials in microfluidic chip channels for the surface-enhanced fluorescence detection of fluorescent dye (SYBR Green I) molecules. Microfluidic chip channels were fabricated by a 248-nm excimer laser. Silver nanoparticles (Ag-NPs) were prepared inside the microfluidic chip channels by directly heating the silver precursor solution. The influence of different temperatures on the sizes of the silver nanoparticles was studied. Then, the surface-enhanced fluorescence technology based on the microfluidic system was used to detect the fluorescent dye molecules. As a result, the fluorescence signal of the fluorescent dye molecules was significantly enhanced by the silver nanoparticles. In addition, the effect of particle size on the fluorescence signal was studied. This simple and fast method is suitable for a fluorescent PCR (polymerase chain reaction) system and has good application prospects for detecting harmful microorganisms in a spacecraft.
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Kurumida, Yoichi, and Nobuhiro Hayashi. "Development of a Novel Q-body Using an In Vivo Site-Specific Unnatural Amino Acid Incorporation System." Sensors 18, no. 8 (August 1, 2018): 2519. http://dx.doi.org/10.3390/s18082519.

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A Q-body capable of detecting target molecules in solutions could serve as a simple molecular detection tool. The position of the fluorescent dye in a Q-body affects sensitivity and therefore must be optimized. This report describes the development of Nef Q-bodies that recognize Nef protein, one of the human immunodeficiency virus (HIV)’s gene products, in which fluorescent dye molecules were placed at various positions using an in vivo unnatural amino acid incorporation system. A maximum change in fluorescence intensity of 2-fold was observed after optimization of the dye position. During the process, some tryptophan residues of the antibody were found to quench the fluorescence. Moreover, analysis of the epitope indicated that some amino acid residues of the antigen located near the epitope affected the fluorescence intensity.
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Guo, Xiang-Qun, Zu-Lin Zhang, Yi-Bing Zhao, Dong-Yuan Wang, and Jin-Gou Xu. "DNA—Dye Fluorescence Enhancement Based on Shifting the Dimer—Monomer Equilibrium of Fluorescent Dye." Applied Spectroscopy 51, no. 7 (July 1997): 1002–7. http://dx.doi.org/10.1366/0003702971941386.

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In this paper, the investigation of DNA–dye fluorescence enhancement based on shifting the dimer–monomer equilibrium of a fluorescent dye, acridine orange (AO), is reported. Formation of a virtually nonfluorescent dimeric dye, acridine orange homodimer (AOAO), induced by the pre-micellar aggregation of an anionic surfactant, sodium dodecyl sulfate (SDS), was observed. The possibility of using the in situ formed AOAO as a fluorescent probe for nucleic acids and polynucleotides was studied. The results showed that a nearly 1000-fold fluorescence enhancement was observed upon addition of calf thymus DNA (CT DNA). The fluorescence enhancement effect of DNA was thought to be based on the DNA modulated shift of the dimmer monomer equilibrium of AO in the anionic surfactant solution. Intercalation of the monomer in DNA caused the dissociation of AOAO and led to a very high fluorescence enhancement. It seemed that the dimeric dye molecules acted as a source of monomer molecules ready for interacting with nucleic acids and, at the same time, decreased the inherent fluorescence of monomer molecules, which proved to be unfavorable to the detection of fluorescence enhancement. A linear dependence of fluorescence intensity on CT DNA concentration over a range from 7.8 ng/mL to 10.0 g/mL, in the presence of AO at a concentration of 1.65 × 10−6mol/L and of SDS at a concentration of 8.0 × 10−4 mol/L, allowed sensitive quantitation of CT DNA in a conventional fluorometer. Calibration graphs for yeast RNA and polynucleotides, such as poly A, poly U, and poly I, were also obtained.
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Fratoddi, Ilaria, Chiara Battocchio, Giovanna Iucci, Daniele Catone, Antonella Cartoni, Alessandra Paladini, Patrick O’Keeffe, Silvia Nappini, Sara Cerra, and Iole Venditti. "Silver Nanoparticles Functionalized by Fluorescein Isothiocyanate or Rhodamine B Isothiocyanate: Fluorescent and Plasmonic Materials." Applied Sciences 11, no. 6 (March 10, 2021): 2472. http://dx.doi.org/10.3390/app11062472.

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This paper presents the synthesis of silver nanoparticles (AgNPs) functionalized with fluorescent molecules, in particular with xanthene-based dyes, i.e., fluorescein isothiocyanate (FITC, λmax = 485 nm) and rhodamine B isothiocyanate (RITC, λmax = 555 nm). An in-depth characterization of the particle–dye systems, i.e., AgNPs–RITC and AgNPs–FITC, is presented to evaluate their chemical structure and optical properties due to the interaction between their plasmonic and absorption properties. UV–Vis spectroscopy and the dynamic light scattering (DLS) measurements confirmed the nanosize of the AgNPs–RITC and AgNPs–FITC. Synchrotron radiation X-ray photoelectron spectroscopy (SR-XPS) was used to study the chemical surface functionalization by structural characterization, confirming/examining the isothiocyanate–metal interaction. For AgNPs–RITC, in which the plasmonic and fluorescence peak are not superimposed, the transient dynamics of the dye fluorescence were also studied. Transient absorption measurements showed that by exciting the AgNPs–RITC sample at a wavelength corresponding to the AgNP plasmon resonance, it was possible to preferentially excite the RITC dye molecules attached to the surface of the NPs with respect to the free dye molecules in the solution. These results demonstrate how, by combining plasmonics and fluorescence, these AgNPs can be used as promising systems in biosensing and imaging applications.
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Liu, Wenjing, Huabin Li, Yanmin Huo, Qingxia Yao, and Wenzeng Duan. "Recent Progress in Research on [2.2]Paracyclophane-Based Dyes." Molecules 28, no. 7 (March 23, 2023): 2891. http://dx.doi.org/10.3390/molecules28072891.

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In recent years, the [2.2]paracyclophane (PCP) ring has attracted extensive attention due to its features of providing not only chirality and electron-donating ability but also steric hindrance, which reduces intermolecular π–π stacking interactions and thereby improves the fluorescence properties of dyes. To date, some circularly polarized luminescence (CPL)-active small organic molecules based on the PCP skeleton have been reviewed; however, the application of the PCP ring in improving the photophysical properties of fluorescent dyes is still limited, and new molecular design strategies are still required. This review summarizes and promotes the application of PCP in fluorescent dye design, fluorescence detection, and CPL modulation. We expect that this review will provide readers with a comprehensive understanding of the PCP skeleton and lead to further improvement in fluorescent dye design.
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8

Middleton, G. W., and B. R. Jennings. "Electrofluorescence of dye-tagged sepiolite." Clay Minerals 26, no. 1 (March 1991): 1–9. http://dx.doi.org/10.1180/claymin.1991.026.1.01.

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AbstractIn electric fields, anisodiametric mineral particles in suspension orientate and align. When tagged with fluorescent molecules, the alignment is accompanied by changes in the intensities of the polarized components of the emitted fluorescence. By measuring these changes under specific experimental conditions, any non-random directional coincidence of the absorption and emission transition moments associated with the dye molecules can be evaluated and the spatial array of the dyes estimated. From such measurements, the binding of the optical brightening agent FBA1, a triazinylaminostilbene compound, to sepiolite has been studied.
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Aristova, D., G. Volynets, S. Chernii, M. Losytskyy, A. Balanda, Yu Slominskii, A. Mokhir, S. Yarmoluk, and V. Kovalska. "Far-red pentamethine cyanine dyes as fluorescent probes for the detection of serum albumins." Royal Society Open Science 7, no. 7 (July 2020): 200453. http://dx.doi.org/10.1098/rsos.200453.

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Benzothiazole based cyanine dyes with bridged groups in the pentamethine chain were studied as potential far-red fluorescent probes for protein detection. Spectral-luminescent properties were characterized for unbound dyes and in the presence of serum albumins (bovine (BSA), human (HSA), equine (ESA)), and globular proteins (β-lactoglobulin, ovalbumin). We have observed that the addition of albumins leads to a significant increase in dyes fluorescence intensity. However, the fluorescent response of dyes in the presence of other globular proteins was notably lower. The value of fluorescence quantum yield for dye bearing a sulfonate group complexed with HSA amounted to 42% compared with 0.2% for the free dye. The detection limit of HSA by this dye was greater than 0.004 mg ml −1 which indicates the high sensitivity of dye to low HSA concentrations. Modelling of structure of the dyes complexes with albumin molecules was performed by molecular docking. According to these data, dyes could bind to up to five sites on the HSA molecule; the most preferable are the haemin-binding site in subdomain IB and the dye-binding site in the pocket between subdomains IA, IIA and IIIA. This work confirms that pentamethine cyanine dyes could be proposed as powerful far-red fluorescent probes applicable for highly sensitive detection of albumins.
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Tran, Vien Thi, and Heongkyu Ju. "Fluorescence Enhancement via Dual Coupling of Dye Molecules with Silver Nanostructures." Chemosensors 9, no. 8 (August 10, 2021): 217. http://dx.doi.org/10.3390/chemosensors9080217.

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We demonstrate the enhancement of fluorescence emitted from dye molecules coupled with two surface plasmons, i.e., silver nanoparticles (AgNPs)-induced localized surface plasmons (LSP) and thin silver (Ag) film supported surface plasmons. Excitation light is illuminated to a SiO2 layer that contains both rhodamine 110 molecules and AgNPs. AgNPs enhances excitation rates of dye molecules in their close proximity due to LSP-induced enhancement of local electromagnetic fields at dye excitation wavelengths. Moreover, the SiO2 layer on one surface of which a 50 nm-thick Ag film is coated for metal cladding (air on the other surface), acts as a waveguide core at the dye emission wavelengths. The Ag film induces the surface plasmons which couple with the waveguide modes, resulting in a waveguide-modulated version of surface plasmon coupled emission (SPCE) for different SiO2 thicknesses in a reverse Kretschmann configuration. We find that varying the SiO2 thickness modulates the fluorescent signal of SPCE, its modulation behavior being in agreement with the theoretical simulation of thickness dependent properties of the coupled plasmon waveguide resonance. This enables optimization engineering of the waveguide structure for enhancement of fluorescent signals. The combination of LSP enhanced dye excitation and the waveguide-modulated version of SPCE may offer chances of enhancing fluorescent signals for a highly sensitive fluorescent assay of biomedical and chemical substances.
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Dissertations / Theses on the topic "Fluorescent Dye Molecules"

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Mangham, Barry. "Synthesis and analysis of fluorescent dye molecules." Thesis, University of Nottingham, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.602528.

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The nature of non-covalent bonding interactions was investigated through the deposition and subsequent scanning tunnelling microscopy (STM) imaging of tetra-substituted porphyrins. Porphyrins bearing iodo, bromo, nitro, pyridyl and carboxylic acid groups were synthesised and deposited on either Au(110) or Au(l11). STM imaging and analysis showed a variety of different orientations and packing for the different functional groups. The unusual tip induced growth of honeycomb packing orientations was seen for tetra-pyridyl substituted porphyrin. Tetra-bromo substituted porphyrin was observed to adopt different ordered orientations of the saddle shape conformation on Au(111). The synthesis of novel porphyrin dimers bearing carboxylic acid groups was investigated, with a variety of different pathways being identified and explored. Furthermore, upon cooling unusual spectroscopic behaviour was observed for a hexa-phenyl substituted meso-linked porphyrin dim er. The synthesis of novel BODIPY dimers and trimers was investigated. A number of fluoro and catecholate substituted BODIPY compounds were synthesised, bearing a variety of different linkers. Linkers investigated included phenyl, biphenyl, terphenyl, durene and terphenylene. Electrochemical and spectroscopic investigations demonstrated a variety of differences between meta- and para-substitution positions. The extension of the linker length from phenyl through to terphenyl displayed a reduction in communication of BODIPY moieties. The durene linked dimer added steric bulk to the centre of the BODIPY dimer, resulting in increased fluorescence lifetimes and quantum yields. 1
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Meyer, Jörg, Anja Wadewitz, Lokamani, Cormac Toher, Roland Gresser, Karl Leo, Moritz Riede, Francesca Moresco, and Gianaurelio Cuniberti. "Molecules for organic electronics studied one by one." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-138788.

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The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-BODIPY molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich
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Meyer, Jörg, Anja Wadewitz, Lokamani, Cormac Toher, Roland Gresser, Karl Leo, Moritz Riede, Francesca Moresco, and Gianaurelio Cuniberti. "Molecules for organic electronics studied one by one." Royal Society of Chemistry, 2011. https://tud.qucosa.de/id/qucosa%3A27781.

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The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-BODIPY molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V.
Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.
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Tsutae, Fernando Massayuki. "Espectroscopia de correlação de fluorescência aplicada em estudos de sistemas moleculares, biológicos e celulares." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-14102016-101124/.

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A espectroscopia de correlação de fluorescência (FCS) é uma das diferentes técnicas de análise por imagens de alta resolução espacial e temporal de biomoléculas em concentrações extremamente baixas. Ela se tornou uma técnica extremamente poderosa e sensível em áreas como bioquímica e biofísica. Como uma técnica bem estabelecida, ela é utilizada para medir concentrações locais de biomoléculas, através da marcação com moléculas fluorescentes. Coeficientes de difusão e constantes cinéticas também podem ser medidos através de FCS assim como detecção de molécula única. Ela também pode dar informação precisa sobre interações de antígeno-anticorpo, ácidos nucleicos e proteínas. Através de uma combinação de marcadores de alto rendimento quântico, fontes de luz estável (lasers), detecção ultrassensível e microscopia confocal, é possível realizar medidas de FCS em volumes de fentolitros (fL) e em concentrações de nanomolar (nM) em soluções aquosas ou em células vivas. Em contraste com outras técnicas de fluorescência, a sensibilidade da FCS aumenta com a diminuição da concentração do fluoróforo marcador, porque o parâmetro de interesse não é a intensidade de emissão de fluorescência, mas sim as flutuações espontâneas da fluorescência. Durante o tempo em que a partícula ou molécula atravessa o volume de medida pode ocorrer mudanças conformacionais e reações químicas e fotofísicas que alteram as características de emissão do fluoróforo e causam flutuações no sinal detectado. Estas flutuações são então monitoradas e transformadas em uma curva de autocorrelação, por intermédio de um software comercial que emprega um modelo físico apropriado para FCS. Em nosso estudo, utilizamos um marcador comercial (ALEXA 488®) para marcar proteínas. Primeiramente utilizamos a técnica de FCS para medir concentrações extremamente baixas de marcadores fluorescentes. Também realizamos um experimento testando a influência da viscosidade do meio na difusão livre do fluoróforo, assim como as melhores condições em que temos um melhor sinal de FCS. Por fim, estudamos a difusão de proteínas marcadas (PUC II e IV) em meio aquoso (PBS) e no interior de células.
Fluorescence correlation spectroscopy (FCS) is one of the many different modes of high-resolution spatial and temporal analysis of extremely low concentrated biomolecules. It has become a powerful and sensitive tool in fields like biochemistry and biophysics. As a well established technique, it is used to measure local concentrations of fluorescently labeled biomolecules, diffusion coefficients, kinetic constants and single molecule studies. Through a combination of high quantum yield fluorescent dyes, stable light sources (lasers), ultrasensitive detection and confocal microscopy is possible to perform FCS measurements in femtoliters volumes and nanomolar concentrations in aquous solution or in live cells. Unlike with other fluorescence technics, its sensibility increases with the decrease of dye concentrarion, because the main factor is not the emission intensity itself. Instead this, spontaneous statistical fluctuation of fluorescence becomes the main factor in FCS analisys. During the time that the conjugated-dye cross the volume detection can occur conformational changes, chemical reaction and photophysical processes that can change the emission properties of the dye and, then, change the detected sinal. This fluctuations are tracked and changed into a autocorrelation curve, by a specific software, appropriate to perform FCS analisys. In our study, we use comercial dye (Alexa 488) to label proteins. Firstly, we applied FCS to measure extremally diluted concentrations of dyes (~1 nM). We have performed experiments testing the influence of the viscosity medium in the free difusion of the dyes and the optical apparatus and conditions that result in the best FCS signal. We also have studied protein diffusion (PUC II e IV) in aquous medium (PBS) and toward the inner of the cells.
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Gösch, Michael. "Microfluidic analysis and parallel confocal detection of single molecules /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-663-4/.

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Kline, Katrina K. Tucker Sheryl A. "Comparison of hyperbranched and dendritic polymers with fluorescent reporter molecules." Diss., Columbia, Mo. : University of Missouri-Columbia, 2009. http://hdl.handle.net/10355/6780.

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The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on March 26, 2010). Thesis advisor: Dr. Sheryl Tucker. Vita. Includes bibliographical references.
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Darko, Janice. "Fluorescent Labeling of Antibiotic Resistant Bacteria Model DNA." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7600.

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Global threats to treatment of bacterial infections due to antibiotic resistance (AR) have been on the rise in recent years. Current diagnostic tests identify bacteria by using blood culture, which takes more than 24 hours. This study focuses on the fluorescent labeling of DNA derived from bacterial AR genes (KPC & VIM) and other model DNAs using oligreen dye (OG) and molecular beacons (MB). A NanoDrop 3300 fluorospectrometer was used to take fluorescence measurements. Linear dynamic range and labeling efficiency were dependent on the following optimized conditions: dilution factor of OG (200 fold), buffer (20 mM Tris HCl, pH 8), and heat treatment of 95 °C for 15 min.Fluorescence analysis of a target DNA with a designed MB showed signal-to-background of 10 with our buffer only and 20 with our buffer and 25% ethanol. I also demonstrated a simple microfluidic device capable of detecting AR genes using model DNAs, magnetic beads, and designed MBs for assays of µ50 L volume. This study provides a first step towards detecting MB-DNA complexes by a simple, low cost, and fast non-amplified method, which may be used to detect AR genes in clinical samples in the future.
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Winstanley, Thomas Peter Llewelyn. "Synthesis and study of fluorescent molecular dyes." Thesis, University of Newcastle upon Tyne, 2013. http://hdl.handle.net/10443/2324.

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Uses for fluorescent dyes are diverse and increasingly important with compounds having many uses in medicinal, chemical and physical fields - amongst others. The creation of new fluorescent dyes helps to push the boundaries of molecular photonics alongside the further study of the underlying principles involved in the systems. This thesis concentrates largely on the synthesis and characterisation aspects of novel fluorescent dyes, though the analysis of the resultant photophysical data also features prominently. Chapter 1 is an introduction to fluorescence from some of the more basic principles involved in the field. A discussion and comparison of intrinsic and extrinsic fluorescent dyes is followed by a brief discussion of a series of examples of fluorescent molecular sensors. As bodipy dyes feature heavily throughout the thesis the second half of the introduction is focused solely on this topic. This half of the chapter centres around the synthetic approaches towards bodipy, modifications to the bodipy core and the resulting photophysics. Photo-induced electron transfer and fluorescence energy transfer is introduced from basic principles along with selected literature examples that demonstrate these processes in systems that incorporate bodipy. Chapter 2 discusses the synthesis and photophysics of a new class of fluorescent dyes based on a highly substituted terephthalate core. The initial aim of the chapter was to create fluorescent systems based on a xanthene core, this was found to be non-fluorescent. As such attention was turned towards a terephthalate intermediate which demonstrated strong and highly red shifted fluorescence in solution, as well as solid state fluorescence. A meso-perfluorinated phenyl ring causes a marked increase in fluorescence quantum yield, along with a pronounced red-shift, relative to the equivalent meso-phenyl variant. This observation lead to a series of Fn-aryl (n = 1,2,3,5) bodipy dyes being synthesised. Chapter 3 subsequently investigates the relationship between the number and position of fluorine atoms on the aryl moiety, and the resultant photophysical measurements. High fluorescence quantum yields were observed with ortho-substitution of fluorine atoms, a trend that was mirrored with the fluorescence lifetime. Mono-ortho fluorine substitution iii of the aryl group was also found to make the bodipy prochiral pathing the way towards axially chiral bodipy compounds. Chapter 4 follows on from chapter 4 by taking prochiral bodipy compounds to there chiral conclusion. In this chapter several synthetic approaches towards axially chiral (AxC) bodipy compounds are discussed. Included in these synthetic approaches is a completely novel route towards asymmetric bodipy cores thus AxC-bodipy compounds. This chapter represents the first examples of AxC bodipy compounds to exist with future developments in the field aimed at enhanced fluorescence sensing in chiral media and facile enantiomeric determination via circularly-polarised fluorescence measurements. Chapter 5 is an in-depth experimental section where the synthesis and characterisation of each compound is detailed. Also provided are the details for each chemical used, purification and drying methods for each solvent used and techniques used for proper characterisation of all of the compounds.
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Lui, Chih-Hung. "Molecular design and synthesis of coumarin fluorescent dyes." Thesis, Heriot-Watt University, 2000. http://hdl.handle.net/10399/572.

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Pauff, Steven M. "Advancements in the Synthesis and Application of Near-Infrared Imaging Reagents: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/751.

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Fluorescence-based imaging techniques provide a simple, highly sensitive method of studying live cells and whole organisms in real time. Without question, fluorophores such as GFP, fluorescein, and rhodamines have contributed vastly to our understanding of both cell biology and biochemistry. However, most of the fluorescent molecules currently utilized suffer from one major drawback, the use of visible light. Due to cellular autofluorescence and the absorbance of incident light by cellular components, fluorescence imaging with visible wavelength fluorophores often results in high background noise and thus a low signal-to-noise ratio. Fortunately, this situation can be ameliorated by altering the wavelength of light used during imaging. Near-infrared (NIR) light (650-900 nm) is poorly absorbed by cells; therefore, fluorophores excited by this light provide a high signal-to-noise ratio and low background in cellular systems. While these properties make NIR fluorophores ideal for cellular imaging, most currently available NIR molecules cannot be used in live cells. The first half of this thesis addresses the synthetic difficulties associated with preparing NIR fluorophores that can be used within living systems. Small molecule NIR fluorophores are inherently hydrophobic which makes them unsuitable for use in the aqueous environment of the cell. Water-solubility is imparted to these dyes through highly polar sulfonates, which subsequently prevents the dyes from entering the cell. The novel work presented here details vii synthetic routes to aid in the development of sulfonated NIR fluorophores, which can be delivered into live cells through the inclusion of an esterase-labile sulfonate protecting group. Application of these synthetic techniques should allow for the development of novel NIR fluorophores with intracellular applications. The second half of this thesis addresses the need for novel NIR imaging reagents. Although several classes of NIR scaffolds do exist, most NIR probes are derivatives of a single class, heptamethine indocyanines. The work described here increases this palette by displaying the ability of NIR oxazines to function as an imaging reagent in live cells and in vivo and as a molecular sensor of biologically-relevant environmental conditions. Combined, the work contained herein has the capacity to not only advance the current NIR toolkit, but to expand it so that fluorescence imaging can move out of the dark and into the NIR light.
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Books on the topic "Fluorescent Dye Molecules"

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Callis, P. R., and A. P. Demchenko. Advanced fluorescence reporters in chemistry and biology I: Fundamentals and molecular design. Heidelberg: Springer, 2010.

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service), ScienceDirect (Online, ed. Single molecule tools: Super-resolution, particle tracking, multiparameter and force based methods. San Diego, CA: Academic Press/Elsevier, 2010.

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Kevin, Foskett J., and Grinstein Sergio, eds. Non-invasivetechniques in cell biology. New York: Wiley-Liss, 1990.

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Kevin, Foskett J., and Grinstein Sergio 1950-, eds. Noninvasive techniques in cell biology. New York: Wiley-Liss, 1990.

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Johnson, Iain D., and Michelle T. Z. Spence. The molecular probes handbook: A guide to fluorescent probes and labeling technologies. [Carlsbad, CA]: Live Technologies Corporation, 2010.

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Kai, Licha, Ntziachristos Vasilis, SPIE (Society), and Optical Society of America, eds. Molecular imaging: 17-18 June 2007, Munich, Germany. Bellingham, Wash: SPIE, 2007.

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Liehr, Thomas. Fluorescence In Situ Hybridization (FISH) — Application Guide. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009.

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Pierre, Bruchez Marcel, and Hotz Charles Z, eds. Quantum dots: Applications in biology. Totowa, N.J: Humana Press, 2007.

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Achilefu, Samuel. Reporters, markers, dyes, nanoparticles, and molecular probes for biomedical applications: 26-29 January 2009, San Jose, California, United States. Bellingham, Wash: SPIE, 2009.

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Raghavachari, Ramesh, and Samuel I. Achilefu. Reporters, markers, dyes, nanoparticles, and molecular probes for biomedical applicaitons II: 25-27 January 2010, San Francisco, California, United States. Bellingham, Wash: SPIE, 2010.

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Book chapters on the topic "Fluorescent Dye Molecules"

1

Stech, Marlitt, Nathanaël Rakotoarinoro, Tamara Teichmann, Anne Zemella, Lena Thoring, and Stefan Kubick. "Synthesis of Fluorescently Labeled Antibodies Using Non-Canonical Amino Acids in Eukaryotic Cell-Free Systems." In Methods in Molecular Biology, 175–90. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1406-8_9.

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AbstractCell-free protein synthesis (CFPS) enables the development of antibody conjugates, such as fluorophore conjugates and antibody-drug conjugates (ADCs), in a rapid and straightforward manner. In the first part, we describe the cell-free synthesis of antibodies containing fluorescent non-canonical amino acids (ncaa) by using pre-charged tRNA. In the second part, we describe the cell-free synthesis of antibodies containing ncaa by using an orthogonal system, followed by the site-specific conjugation of the fluorescent dye DyLight 650-phosphine. The expression of the antibodies containing ncaa was analyzed by SDS-PAGE, followed by autoradiography and the labeling by in-gel fluorescence. Two different fluorescently labeled antibodies could be generated.
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Vorobjev, Ivan A., Aigul Kussanova, and Natasha S. Barteneva. "Development of Spectral Imaging Cytometry." In Methods in Molecular Biology, 3–22. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3020-4_1.

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AbstractSpectral flow cytometry is a new technology that enables measurements of fluorescent spectra and light scattering properties in diverse cellular populations with high precision. Modern instruments allow simultaneous determination of up to 40+ fluorescent dyes with heavily overlapping emission spectra, discrimination of autofluorescent signals in the stained specimens, and detailed analysis of diverse autofluorescence of different cells—from mammalian to chlorophyll-containing cells like cyanobacteria. In this paper, we review the history, compare modern conventional and spectral flow cytometers, and discuss several applications of spectral flow cytometry.
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Voelzmann, André, and Natalia Sanchez-Soriano. "Drosophila Primary Neuronal Cultures as a Useful Cellular Model to Study and Image Axonal Transport." In Methods in Molecular Biology, 429–49. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1990-2_23.

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AbstractThe use of primary neuronal cultures generated from Drosophila tissue provides a powerful model for studies of transport mechanisms. Cultured fly neurons provide similarly detailed subcellular resolution and applicability of pharmacology or fluorescent dyes as mammalian primary neurons. As an experimental advantage for the mechanistic dissection of transport, fly primary neurons can be combined with the fast and highly efficient combinatorial genetics of Drosophila, and genetic tools for the manipulation of virtually every fly gene are readily available. This strategy can be performed in parallel to in vivo transport studies to address relevance of any findings. Here we will describe the generation of primary neuronal cultures from Drosophila embryos and larvae, the use of external fluorescent dyes and genetic tools to label cargo, and the key strategies for live imaging and subsequent analysis.
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Haidekker, Mark A., Matthew Nipper, Adnan Mustafic, Darcy Lichlyter, Marianna Dakanali, and Emmanuel A. Theodorakis. "Dyes with Segmental Mobility: Molecular Rotors." In Springer Series on Fluorescence, 267–308. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-04702-2_8.

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Koreivienė, Judita. "Microalgae Lipid Staining with Fluorescent BODIPY Dye." In Methods in Molecular Biology, 47–53. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/7651_2017_101.

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Turner, Linda, and Howard C. Berg. "Labeling Bacterial Flagella with Fluorescent Dyes." In Methods in Molecular Biology, 71–76. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7577-8_7.

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Czekanska, Ewa M. "Assessment of Cell Proliferation with Resazurin-Based Fluorescent Dye." In Methods in Molecular Biology, 27–32. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-108-6_5.

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EcheverrÍa Aitken, Colin, R. Andrew Marshall, and Joseph D. Pugi. "Improved Dye Stability in Single-Molecule Fluorescence Experiments." In NATO Science for Peace and Security Series B: Physics and Biophysics, 83–99. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-90-481-2368-1_6.

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Aussenegg, F. R., A. Leitner, M. E. Lippitsch, and H. Reinisch. "Fluorescence Lifetime of Dye Molecules Near a Metal Surface." In Ultrafast Phenomena VI, 434–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-83644-2_123.

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Petrov, E. P., V. N. Bogomolov, I. I. Kalosha, and S. V. Gaponenko. "Fluorescence of Dye Molecules Embedded in a Photonic Crystal." In Springer Series in Chemical Physics, 523–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-72289-9_157.

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Conference papers on the topic "Fluorescent Dye Molecules"

1

Harris, T. D., J. J. Macklin, J. K. Trautman, and L. E. Brus. "Imaging and Time-Resolved Spectroscopy of Single Molecules." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/lacea.1996.lwd.5.

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Recent progress in the fluorescence detection of individual molecules [1-8] suggests that a single dye molecule can be a useful tool to probe chemical identity and activity. Measurement of fluorescence lifetime [5,6] and spectrum [6] can be augmented by knowledge of molecular orientation using polarized light [3], and triplet [2] and photoisomer excitation, as well as diffusion processes, via fluorescence-intensity correlation. Applications of fluorescent probes include the study of the dynamic conformation of membrane-bound proteins, transport of and signaling by messenger molecules, and the optical detection of the sequence of DNA. While molecules can be spatially located using near-field microscopy [5-8], near-field probes can perturb the molecule under study. We show here that molecular properties can be determined easily and in a non-perturbative manner using far-field illumination, and we obtain unperturbed spectral and lifetime data that cannot be extracted from an ensemble measurement.
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Canva, M., P. Georges, A. Dubois, A. Brun, F. Chaput, and J. P. Boilot. "Tunable dye-doped xerogel lasers." In The European Conference on Lasers and Electro-Optics. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/cleo_europe.1994.cwc1.

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The easiest route to produce tunable optical pulses is to use a broadband fluorescent gain medium. For this purpose organic dye molecules are very suitable and have been widely used in solution during the past 30 years. Today, new crystals such as titanium sapphire, and nonlinear techniques such as optical parametric oscillation, may provide solid state systems. For dyes to remain competitive, it would be interesting to disperse the molecules in solid host matrices, instead of diluting them in solutions. This may be achieved by using the sol-gel process.1–3
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Castro, Alonso, Frederic Fairfield, and Brooks Shera. "Ultrasensitive detection of single DNA molecules." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/oam.1992.thw9.

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We report on the detection of single lambda DNA molecules in flowing TBE buffer. DNA molecules at 10−14 M bound the fluorescent dye ethidium bromide at 10−10 M and were detected by using our recently developed technique for single molecule detection. This technique involves repetitive excitation of individual fluorophores with a frequency-doubled Nd:YAG laser, fluorescence detection with a microchannel-plate photo-multiplier based time-correlated single-photon counter, and signal processing with time-gated discrimination electronics. This detection takes 50 ms in a sample volume of 3.5 pL through which the DNA molecules pass at a rate of about 1 per second. The fluorescence lifetime of ethidium bromide increases from 1 to 24 ns when it becomes intercalated in DNA. To ensure that only DNA molecules were detected, we set a time window from 5 to 10 ns after the arrival of the laser pulse, thus rejecting both prompt scattering and fluorescence from free EtdBr molecules. The present method is at least 1000 times as sensitive as current flow cytometry methods. Quantitation of the fluorescence intensity will allow us to determine the lengths of individual DNA molecules, which can lead to the development of separation and size sorting techniques that are much faster than present methods.
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Campione, Salvatore, and Filippo Capolino. "Metamaterials based on plasmonic nanoshells and loss-compensation using fluorescent dye molecules and quantum dots." In SPIE OPTO, edited by Ali Adibi, Shawn-Yu Lin, and Axel Scherer. SPIE, 2012. http://dx.doi.org/10.1117/12.909569.

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Brewer, Bryson, Yandong Gao, and Deyu Li. "A Study of Small Molecule Absorption in Polydimethylsiloxane." In ASME 2012 Third International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/mnhmt2012-75105.

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While polydimethylsiloxane (PDMS) has proven to be a popular material in the construction of microfluidic devices, the polymer network structure of PDMS makes it permeable to some molecules. This feature can be problematic for applications where thin PDMS walls are used to separate two different molecular streams or cell populations. Therefore, a better understanding of factors affecting small molecule absorption in PDMS is important for better design and operation of microfluidic devices. We report on studies of various factors in the absorption of fluorescent dyes in PDMS. Results show significant effects of thermal aging of PDMS on the absorption of the hydrophobic molecule Nile Red. In addition, the short-term hydrophobic recovery of the PDMS devices after being plasma bonded to a glass slide was investigated. Furthermore, we have tested the effects of aspiration and flushing, which show that the wetting property (hydrophilic or hydrophobic) of the flushing solvents can significantly affect the absorption of the Nile Red dye. Finally, parallel tests of PDMS absorption of fluorescein isothiocyanate (FITC) were conducted with no absorption observed.
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Lee, Wing-Kee, Ali Gungor, and Christopher C. Davis. "Photothermal studies of nonradiative energy loss in dilute dye solutions." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1985. http://dx.doi.org/10.1364/oam.1985.ft8.

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Single-frequency laser heterodyne measurements in a modified Jamin interferometer have been used to study the nonradiative energy loss of isolated rhodamine 6G molecules in solution. Pure methanol and several methanol-based solvents containing the quencher potassium iodide were studied. Simultaneous measurement of both the fluorescent intensity and the photothermal phase modulation induced by AM argon-ion laser excitation allows absolute determination of both the quantum efficiency η and the fraction of absorbed photoenergy converted to heat. Broadband fluorescent intensity was measured with a photodiode. Photothermal phase modulation was synchronously detected by operating the Jamin interferometer in quadrature and passing the resultant linear intensity modulation to a lock-in amplifier. Rhodamine 6G concentration as low as 5 × 10−9 g/m liter could be used. Typical Kl quencher concentrations were in the 0.33-4.5-mg/m liter range. The absolute quantum efficiency of rhodamine 6G at zero quencher concentration was found to be 96 %. The fraction of absorbed energy converted to heat at zero quencher concentration was 12%.
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Sklar, Larry A., Gregory M. Jones, and Terri Gilbert Houghton. "Cellular and Biological Applications of Laser Induced Fluorescence." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.thc.1.

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Lasers are widely used in biological applications to detect fluorescent molecules which probe the structure and activities of cells, cellular components, and biomolecules. Dye molecules used in biological systems are often referred to as “probe molecules” or “probes”. Lasers are often selected over other excitation sources such as arc lamps because of the power density, the increased intensity when imaging faint or dilute fluorophores and the advantages of monochromatic sources for reducing stray light from turbid biological samples. The applications introduced in this paper include observing molecules and cells in suspension by spectroscopy, flow cytometry, and microscopy.
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Zhang, H., A. M. Jonkman, P. van der Meulen, and M. Glasbeek. "Femtosecond Studies of Charge Separation in the Fluorescent State of DCM." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.md.7.

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Solvation dynamics has long been recognized to be of great importance for the understanding of the rate of intramolecular electron transfer (ET) reactions1,2. Especially when the ET reaction takes place in the so-called strong adiabatic coupling limit, solvation dynamics may predominantly determine the ET rate constant. Under such conditions one has κ ≫ 1, where the adiabaticity parameter3, κ, is given by κ = π V2 〈τ〉 /ħλm, in which V is the electronic coupling between the locally excited (LE) and charge transfer (CT) states involved in the electron transfer process, 〈τ〉 is the solvent relaxation time and λm is the solvent reorganization energy. Recently, for a number of molecules solvent controlled ET in the photo-excited state has been considered in the strong adiabatic coupling regime4. In this report, we present results of a femtosecond pump-probe study of the charge separation reaction in the photo-excited state of a large laser dye molecule, 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4-H-pyran (DCM). We have performed a subpicosecond study of the solvatochromism of the DCM molecule. A major finding is that following the pulsed excitation of the molecule, the integrated intensity of the spontaneous fluorescence exhibits a transient decay to approximately 50% of its initial value in a few picoseconds. The results are consistent with strongly mixed LE and the CT excited states for DCM (i.e., the adiabatic coupling limit applies) so that the solvation dynamics constitutes the rate determining step in the ET process.
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Hébert, P., G. Baldacchino, T. Gustavsson, V. Kabelka, P. Baldeck, and J. C. Mialocq. "Subpicosecond Study of the Dynamic Processes in Push-Pull Styrenes and the Role of Solvation." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.fc10.

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A great deal of attention has recently been devoted to the role of solvation in chemical reactions involving intramolecular charge transfer, LE (locally excited)-TICT (twisted intramolecular charge transfer) singlet excited state relaxation and trans-cis photoisomerization. In this paper we present a subpicosecond study of the solvation dynamics of the styryl 8 laser dye (2-(4-(4-dimethylaminophenyl)-1,3-butadienyl)-3-ethylbenzothiazolium perchlorate) in various solvents. Our results are discussed in the light of recent studies of styryl 7 [1,2] and of our previous studies of the solvatochromism of DCM (4-(dicyanomethylene)-2-methyl-6-[p-(dimethylaminostyryl)-4H-pyran]) [3,4]. Both styryls are remarkable as regards the weak overlap between their absorption and emission spectra. The large Stokes shift observed in DCM is related to a strong intramolecular charge transfer between the electron donor dimethylamino group and the electron acceptor dicyanomethylene group. However, the behavior of the two styryls with respect to solvent polarity is quite different. On the one hand, the neutral DCM presents a red shift of its absorption transition energy with increasing solvent polarity which is due to the feeble solvation of the electronic ground state and the strong response of the electronic polarization of the solvent molecules to the solute Franck-Condon electronic excitation. Its fluorescence spectrum shows a large dependency with respect to the solvent polarity indicating a strong increase of the dipole moment upon electronic excitation [3,4]. On the other hand, in the cationic styryl 8 molecule, an unsymmetrical polymethine-cyanine, the large blue shift of the absorption maxima in solvents of increasing polarity indicates the enormous stabilization of the electronic ground state with respect to the Franck-Condon excited singlet state. The subsequent relaxation of the fluorescent excited state is only minor as shown by the small variation of the wavelengths of the styryl 8 fluorescence maxima with solvent polarity. We thus infer that the dipole moment of the fluorescent state and its solvent cage are weakly affected upon electronic excitation.
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Ammermann, Dirk, Achim Böhler, Christoph Rompf, and Wolfgang Kowalsky. "Double Heterostructure and Multiple Quantum Well Organic Light Emitting Diodes for Flat Panel Displays." In Organic Thin Films for Photonic Applications. Washington, D.C.: Optica Publishing Group, 1995. http://dx.doi.org/10.1364/otfa.1995.tua.3.

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Multilayer organic light emitting diodes (OLEDs) have recently been intensively studied [1,2] for future applications in large-area flat panel color displays. The principle of operation is similar to that of inorganic light emitting diodes (LEDs). Holes and electrons are injected from opposite electrodes into the organic layer sequence and recombine generating singlet excitons that decay radiatively. The emission layer consists of highly fluorescent organic dye molecules sandwiched between separate hole and electron transport layers. This multilayer structure allows to achieve bright electroluminescent emission in the visible spectral region at low driving voltages. We discuss the growth and characterization of high brightness double heterostructure diodes in the green spectral region and present results obtained from organic multiple quantum well light emitting diodes.
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Reports on the topic "Fluorescent Dye Molecules"

1

Basche, Th, and W. E. Moerner. Photon Antibunching in the Fluorescence of a Single Dye Molecule Trapped in a Solid. Fort Belvoir, VA: Defense Technical Information Center, June 1992. http://dx.doi.org/10.21236/ada252261.

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Garnica Montaña, Johanna Paola, Oscar Jair Rodríguez Rodríguez, and Franco Alirio Vallejo Cabrera. Caracterización molecular del germoplasma de arracacha (Arracacia xanthorrhiza Bancr.) en Colombia mediante marcadores SSRs fluorescentes. Corporación colombiana de investigación agropecuaria - AGROSAVIA, 2020. http://dx.doi.org/10.21930/agrosavia.poster.2020.3.

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La arracacha (Arracacia xanthorrhiza Bancr.) es una raíz tuberosa originaria de los Andes, con mayor área de cultivo en Brasil, seguido de Colombia, Ecuador y Venezuela. Esta especie es la única umbelífera domesticada de las Américas y se considera que Colombia, Ecuador y Perú son los centros de diversidad primaria del género y conservación de la especie. Sin embargo, no existe información concreta sobre diversidad genética de A. xanthorrhiza en Colombia. Por lo tanto, abordamos un análisis de diversidad genética a nivel morfológico y molecular de 93 accesiones de arracacha manejadas por el Sistema de Bancos de Germoplasma de la Nación para la Alimentación y la Agricultura (SBGNAA).
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Ardakani, O. H. Organic petrography and thermal maturity of the Paskapoo Formation in the Fox Creek area, west-central Alberta. Natural Resources Canada/CMSS/Information Management, 2022. http://dx.doi.org/10.4095/330296.

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The Paskapoo Formation, which ranges in age from middle to upper Paleocene, is the major shallow aquifer in Alberta. This study is part of a larger GSC-led study on the potential environmental impact of hydrocarbon development in the Fox Creek area (west-central Alberta) on shallow aquifers. Fox Creek is located near the northern limit of the Paskapoo Formation. In addition to the underlying organic-rich source rocks in the study area, including the Duvernay Formation that is currently exploited for hydrocarbon resources, the Paskapoo Formation contains organic-rich intervals and coal seams. In order to investigate any potential internal hydrocarbon sources within the Paskapoo Formation, ninety-seven (97) cutting samples from the formation obtained from eight shallow monitoring wells (50-90 m) in the study area were studied for total organic carbon (TOC) content, organic matter composition and thermal maturity of coal seams using programmed pyrolysis analysis and organic petrography. The TOC content of all samples ranges from 0.2 to 8.8 wt. %, with a mean value of 0.95 ± 1.6 wt. % (n=97). The Tmax values of studied samples range from 347 to 463 °C, with a mean value of 434 ± 20 °C that suggest a range of thermal maturity from immature to peak oil window. The random reflectance (Rr) measurement and fluorescence microscopy on eighteen (18) selected samples with TOC content > ~1 wt. % shows a mean Rr value of 0.27% and 0.42% for the overlying till deposits and the underlying shallow depth sandstone, siltstone, shale and coal seams respectively, indicating a low rank coal ranging from lignite to sub-bituminous coal. Blue to green and yellow fluorescing liptinite macerals further confirmed the low maturity of studied samples. The low S2 yield of a large part of the samples (65%) resulted in unreliable Tmax values that overestimated the thermal maturity. Although the organic matter in the studied intervals are immature, exsudatinite, as secondary liptinite maceral, was observed in samples from the lower parts of the studied monitoring wells. Exsudatinite generally derives from the transformation of sporinite, alginite, resinite and varieties of vitrinite, which is a resinous or asphalt like material. Considering the thickness and distribution of coal seams in the studied samples, it is unlikely the exsudatinite will be a major source for aquifer hydrocarbon contamination in the study area. Additional stratigraphic studies and molecular geochemical analysis could provide an estimate of the total volume of possible organic compounds contribution to the aquifer in the study area. Due to the presence of coal seams in the studied intervals of the Paskapoo Formation, it is important to investigate the possibility of biogenic methane formation in Paskapoo shallow aquifers.
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