Download or read book Design and Synthesis of Fluorescent Dyes for Use in Proteomic Research written by Kevin James Spicka and published by . This book was released on 2008 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics is a rapidly developing field requiring powerful new technology in order to be able to detect proteins at increasingly lower concentrations. To aid in the detection of proteins at lower concentrations, DIGE dyes, a family of spectrally resolved fluorescent dyes, are currently available to proteomic researchers for 2D gel analysis. However, the demands of protein detection dictate that dyes that are even more sensitive and versatile be created. The syntheses of highly sensitive, water soluble BODIPY fluorophore dyes are described. These dyes are proposed to have the necessary sensitivity to allow for detection of proteins in much lower concentrations, providing an improvement over current protein detection limits. The BODIPY dyes that have been synthesized are available in a variety of absorbances and emissions. While fluorescent dyes that are amine-reactive are the most popular covalently binding protein labeling markers being used in today's proteomic research, thiol-reactive fluorescent markers are gaining importance in proteomic research. Since thiol residues are less common in proteins compared to their amine counterparts, saturation labeling and quantification are more easily achieved. The syntheses of sensitive thiol- reactive fluorescent dyes are described. These syntheses allow for quick generation of thiol-reactive fluorescent markers to be used in proteomic research.
Download or read book Synthesis of Zwitterionic Cyanine Dyes for Use in Proteomics written by Mark Galen Epstein and published by . This book was released on 2012 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: The CyDye family of fluorescent dyes are the tools currently in use today for applications in two dimensional difference gel electrophoresis (2D-DIGE) techniques. The lysine labeling CyDyes are limited by problems with over labeling resulting in protein precipitation and isoelectric point (pI) drift at high pH's. These limitations have been addressed by a family of highly water soluble and pI balancing zwitterionic BODIPY dyes, which were previously synthesized in the Grieco group. The absorbance maxima of the BODIPY fluorophores were tuned through extension of the pi system to produce a three color, spectrally resolved dye set. However the fluorescence of the green emitting BOPIDY suffered at pH's less than 3.5 and greater than 11, while the red emitting BODIPY was susceptible to Michael addition changing its emission profile. To address the limitations of the BODIPY family of dyes, a new family of zwitterionic 2DDIGE dyes based on the established CyDye fluorophores have been synthesized. A complete three dye zwitterionic minimal labeling set which features a cysteic acid motif, titratable amine functionality and an NHS activated ester group reactive towards lysine residues has been synthesized: Z-Cy2 (QY= 6.8% ± 0.1, epsilon= 155,000), Z-Cy3 (QY= 11.1% ± 0.4, epsilon= 124,500), Z-Cy5 (QY= 43.3% ± 0.6, epsilon= 217,600). In addition, a complete three dye zwitterionic saturation labeling set which incorporates a cysteic acid motif and maleimide functionality reactive towards cysteine residues has also been synthesized: Z-Cy2-Mal (QY= 6.6 % ± 0.1, epsilon= 104,500), Z-Cy3-Mal (QY= 12.4 % ± 0.5, epsilon= 127,700), Z-Cy5-Mal (QY= 40.2 % ± 0.4, epsilon= 217,400).
Download or read book Advanced Fluorescence Reporters in Chemistry and Biology I written by Alexander P. Demchenko and published by Springer Science & Business Media. This book was released on 2010-09-08 with total page 393 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence reporter is the key element of any sensing or imaging technology. Its optimal choice and implementation is very important for increasing the sensitivity, precision, multiplexing power, and also the spectral, temporal, and spatial reso- tion in different methods of research and practical analysis. Therefore, design of ?uorescence reporters with advanced properties is one of the most important problems. In this volume, top experts in this ?eld provide advanced knowledge on the design and properties of ?uorescent dyes. Organic dyes were the ?rst ?uorescent materials used for analytical purposes, and we observe that they retain their leading positions against strong competition of new materials – conjugated polymers, semiconductor nanocrystals, and metal chelating complexes. Recently, molecular and cellular biology got a valuable tool of organic ?uorophores synt- sized by cell machinery and incorporated into green ?uorescent protein and its analogs. Demands of various ?uorescence techniques operating in spectral, anisotropy, and time domains require focused design of ?uorescence reporters well adapted to these techniques. Near-IR spectral range becomes more and more attractive for various applications, and new dyes emitting in this range are strongly requested. Two-photonic ?uorescence has become one of the major tools in bioimaging, and ?uorescence reporters well adapted to this technique are in urgent need. These problems cannot be solved without the knowledge of fundamental principles of dye design and of physical phenomena behind their ?uorescence response.
Download or read book Molecular Design and Synthesis of High Performance Fluorescent Dyes for Textile Applications written by Mohammed Saiful Islam and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fluorescent Analogs of Biomolecular Building Blocks written by Marcus Wilhelmsson and published by John Wiley & Sons. This book was released on 2016-04-04 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescent Analogs of Biomolecular Building Blocks focuses on the design of fluorescent probes for the four major families of macromolecular building blocks. Compiling the expertise of multiple authors, this book moves from introductory chapters to an exploration of the design, synthesis, and implementation of new fluorescent analogues of biomolecular building blocks, including examples of small-molecule fluorophores and sensors that are part of biomolecular assemblies.
Download or read book Design Synthesis and Characterization of Mechanosensitive Dual Fluorescent Dyes as Potential Probes for Biological Applications written by Susantha Ganegamage and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter 3 of this dissertation explores a hypothesis that leverages the seesaw photophysical model for N-aryl (2,3- and 1,8-) naphthalimides. The Heagy group initially developed this model to understand the dual fluorescence effect concerning the electron donor or electron-withdrawing substituents. This study envisions the design and synthesis of novel dual fluorescence molecules for a new class of N-aryl-phenanthridinone dyes. The applied photophysical model further investigates these dyes with a substitution pattern opposite naphthalimide systems. Interestingly, predictive computational modeling shows that the substituent pattern, used previously for 2,3-naphthalimides, relies on these groups getting placed on rings in opposite positions for N-aryl-phenanthridinones. Chapter 4, provides an overall conclusion of the and future directions for both parts of the research. In chapter 5, a complete description of experimental data is provided for the characterization of all the dye systems presented. This data includes a detailed synthesis procedure, characterization, purity analysis by HPLC, absorptivity calculation, fluorescence lifetime measurements, quantum yield determination, biological evaluation and fluorescence titration.
Download or read book Molecular Design and Synthesis of Coumarin Fluorescent Dyes written by Chih Hung Lui and published by . This book was released on 2000 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Synthesis of Fluorescent and Phosphorescent Dyes for Biochemical Application written by Elizabeth Ann Sanger and published by . This book was released on 2010 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current dyes for proteomics that are applicable to multiplexing experiments suffer from lack of sensitivity and poor water solubility. A series of tetramethyl rhodamine derivatives were developed to study the effects of substitution patterns on the photophysical properties of the fluorophores. After identifying the superior fluorophore a zwitterionic side chain with properties beneficial for two dimensional applications was coupled to the fluorophore and the photophysical properties were studied. Iridium(III) cationic fluorophores are interesting synthetic targets due to their ultraviolet absorption wavelengths and visible emission properties. A series of Iridium(III) fluorophores, some of which contain a handle for further synthetic extension, has been made to study the ligand effects on the emission properties of the dyes. Finally, some of these dyes have been synthetically modified for proteomic labeling applications.
Download or read book Design and Synthesis of Fluorescent Probes written by Prabin Rai and published by . This book was released on 2013 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: The fundamental objective of this project is to design, synthesize, and characterize fluorescent dyes, which may be utilized in super resolution imaging techniques. In Chapters 1, 2 and 3, we concentrated on photoswitchable rhodamine dyes. We synthesized several rhodamine dyes and increased their water solubility, installed a bioconjugation unit and, more importantly, we optimized the absorption properties (close to 400 nm) of the rhodamine spirolactams in their closed state and studied their basic photophysical properties as well. In Chapter 4, we synthesized azido-DCDHF fluorogens that can be converted to the bright state after a 1,3-dipolar cycloaddition reaction between an azide-Ph-DCDHF and a strained alkene. We synthesized some strained alkenes, which may speed up the kinetics in 1,3-dipolar cycloaddition. This chemical method of turning the dyes from dark to bright state is a new dimension in the bioconjugation arena. In Chapter 5, we synthesized Nile red derivatives which can switch to a bright state from a dark state by collision on the cell surface utilizing PAINT methodology. We expected that the design of new Nile red derivatives may have better properties than the parent Nile red. Besides the PAINT technique, we worked on some active control of emission by enzymatic cleavage of fluorescent dyes in a dark state to the bright state, which can be utilized in super resolution imaging. Related to the 1,3-dipolar cycloaddition reaction between azido-DCDHF and norbornene, we have examined recently popularized tetrazine chemistry. We linked pyridyl tetrazines to DCDHF with short spacer. In Chapter 6, we describe the preparation of co-crystals between perfluorophenazine and several polynuclear aromatic compounds/polynuclear heteroaromatic compounds. In Chapter 7 we describe the preparation of some partially fluorinated heteropolynuclear aromatic compounds such phenzaine and acridine class of compounds for possible use in organic semiconductors.
Download or read book Design Syntheses and Applications of Fluorescent Dyes written by Liangxing Wu and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: New methodologies for the efficient syntheses of 4,4-difluoro-4-bora-3a,4adiaza- s-indacenes (BODIPYs) and rosamines were developed. A serendipitous discovery led to a new reaction which afforded BODIPYs in high yields. Systematic studies of the kinetics and mechanisms of the new reaction were performed. A series of BODIPYs were successfully prepared using the new approach. A simple and efficient synthesis of rosamines with cyclic-amine substituents was devised. These new rosamines showed interesting anti-tumor activities. Several types of novel fluorescent compounds were prepared. Highly fluorescent GFP-chromophore analogs were designed and synthesized. The correlation between the optical properties and the structures was investigated. New pyronin dyes with mesoheteroatom substituents were efficiently prepared. The fluorescence properties of these compounds were highly dependent on the nature of the meso-substituents. A set of BODIPY dyes that fluoresce brightly above 600 nm were made. They were then used as acceptors to prepare water-soluble through-bond energy transfer cassettes. All the cassettes had complete energy transfer and high quantum yields in MeOH. A few also had good fluorescence properties in aqueous media and even on proteins. The through-bond energy transfer cassettes were used to monitor protein-protein interactions. In order to test our hypothesis, an artificial protein interaction system was built by utilizing the biotin/(strept)avidin interactions. Thus Atto425-BSA-biotin, streptavidin-cassette1 and avidin-cassette2 were prepared. The interactions between Atto425-BSA-biotin and cassette labeled (strept)avidin were successfully detected in vitro and in living cells by fluorescence techniques.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2009 with total page 810 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Handbook of Fluorescent Dyes and Probes written by R. W. Sabnis and published by John Wiley & Sons. This book was released on 2015-06-02 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: A COMPLETE, UP-TO-DATE RESOURCE OF INFORMATION ON MORE THAN 150 FLUORESCENT DYES AND PROBES Handbook of Fluorescent Dyes and Probes is the most comprehensive volume available on the subject, covering all the available dyes and probes known to date in the literature for uses in various fields. Top dye expert Dr. Ram Sabnis organizes the compounds alphabetically by the most commonly used chemical name. He presents an easy-to-use reference complete with novel ideas for breakthrough research in medical, biological, chemical, color, material, physical and related allied fields. The ease of use of the handbook is further enhanced by various appendixes provided at the end of the book to conveniently and easily locate the dye as per the reader's need. This is the first book to give the CAS registry numbers, chemical structure, Chemical Abstract (CA) index name, all other chemical names, Merck Index number, chemical/dye class, molecular formula, molecular weight, physical form, solubility, melting point, boiling point, pKa, absorption maxima, emission maxima, molar extinction coefficient, and quantum yield of fluorescent dyes and probes, as well as to provide access to synthetic procedures (lab scale and industrial scale) of dyes and probes in a single source. This user-friendly handbook also features references on safety, toxicity and adverse effects of dyes and probes on humans, animals and the environment, including: acute/chronic toxicity aquatic toxicity carcinogenicity cytotoxicity ecotoxicity genotoxocity hematotoxicity hepatotoxicity immunotoxicity marine toxicity microbial toxicity mutagenicity nephrotoxicity neurotoxicity nucleic acid damage oral toxicity phototoxicity phytotoxicity reproductive toxicity skin toxicity Containing imaging/labeling applications, biological/medical applications and industrial applications, Handbook of Fluorescent Dyes and Probes is a convenient, vital resource for industrial and academic researchers, and a valuable desktop reference for medical professionals, lab supervisors, scientists, chemists, biologists, engineers, physicists, intellectual property professionals, students, and professors. Includes all fluorescent dyes & probes known to date and provides a complete, up-to-date library of information in one reference/handbook Includes more than 300 fluorescent dyes & probes organized alphabetically by the commonly used Chemical Name Provides access to synthesis procedures (lab scale and industrial scale) of fluorescent dyes & probes First book to provide references on safety, toxicity and adverse effects of fluorescent dyes and probes on humans, animals, and the environment User-friendly and convenient resource guide for chemical, biological, medical, and intellectual property professionals in a broad range of disciplines
Download or read book Design Synthesis and Characterization of New Two photon Absorbing 2PA Fluorescent Dyes and Bioconjugates and Their Applications in Bioimaging written by Carolina D. Andrade and published by . This book was released on 2010 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The development of new multiphoton absorbing materials has attracted the attention of researchers for the last two decades. The advantages that multiphoton absorbing materials offer, versus their one-photon absorbing counterparts, rely on the nature of the nonlinearity of the absorption process, where two photons are absorbed simultaneously offering increased 3D resolution, deeper penetration, and less photobleaching and photodamage as a result of a more confined excitation. The applications of efficient two-photon absorbing materials have been extensively expanding into the fields of photodynamic therapy, microscopy, and optical data storage. One of the fields where an increased interest in multiphoton absorbing materials has been most evident is in bioimaging, in particular, when different cellular processes and organelles need to be studied by fluorescence microscopy. The goal of this research was to develop efficient two-photon absorption (2PA) compounds to be used in fluorescence bioimaging, meaning that such compounds need to posses good optical properties, such as high fluorescence quantum yield, 2PA cross section, and photostability. In the first chapter of this dissertation, we describe the synthesis and structural characterization of a new series of fluorescent donor-acceptor and acceptor-acceptor molecules based on the fluorenyl ring system that incorporated functionalities such as alkynes and thiophene rings, through efficient Pd-catalyzed Sonogashira and Stille coupling reactions, in order to increase the length of the conjugation in our systems. These new molecules proved to have high two-photon absorption (2PA), and the effect of these functionalities on their 2PA cross section values was evaluated. Finally, their use in two-photon fluorescence microscopy (2PFM) imaging was demonstrated. One of the limitations of the compounds described in Chapter 1 was their poor water solubility; this issue was addressed in Chapter 2. The use of micelles in drug delivery has been shown to be an area of increasing interest over the last decade. In the bioimaging field, it is key to have dye molecules with a high degree of water solubility to enable cells to uptake the dye. By enclosing a hydrophobic dye in Pluronic® F-127 micelles, we developed a system that facilitates the use of 2PA molecules (typically hydrophobic) in biological systems for nonlinear biophotonic applications, specifically to image the lysosomes. Furthermore, we report in this chapter the efficient microwave-assisted synthesis of the dye used in this study. In addition, linear photophysical and photochemical parameters, two-photon absorption (2PA), and superfluorescence properties of the dye studied in Chapter 2, were investigated in Chapter 3. The steady-state absorption, fluorescence, and excitation anisotropy spectra of this dye were measured in several organic solvents and aqueous media. In Chapter 4, we describe the preparation and the use of an efficient and novel two-photon absorbing fluorescent probe conjugated to an antibody that confers selectivity towards the vascular endothelial growth factor receptor 2 (VEGFR-2) in porcine aortic endothelial cells that express this receptor (PAE-KDR). It is known that this receptor is overexpressed in certain cancer processes. Thus, targeting of this receptor will be useful to image the tumor vasculature. It was observed that when the dye was incubated with cells that do not express the receptor, no effective binding between the bioconjugate and the cells took place, resulting in very poor, nonspecific fluorescence images by both one and two-photon excitation. On the other hand, when the dye was incubated with cells that expressed VEGFR-2, efficient imaging of the cells was obtained, even at very low concentrations (0.4[micrometer]). Moreover, incubation of the bioconjugate with tissue facilitated successful imaging of vasculature in mouse embryonic tissue.
Download or read book Systematic Exploration of Indolizine Based Small Fluorescent Molecules written by Youngjun Lee and published by Springer Theses. This book was released on 2019-09-11 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis describes an in-depth study of an indolizine-based fluorophore, from understanding of its structure-photophysical property relationship to its application as a useful biological reporter. Organic fluorophores have been extensively used in the field of molecular biology owing to their excellent photophysical property, suitable cell permeability, and synthetic flexibility. Understanding of the structure-photophysical property relationship of a given fluorophore often paves the road to the development of valuable molecular probes to visualize and transcribe biological networks. In this thesis, respective chapters deal with molecular design, organic synthesis, structure-property analysis, and quantum-mechanical interpretation of unexplored family of indolizine-based molecules. This systematic exploration has led to rational development of a new microalgae lipid droplet probe, colorful bioorthogonal fluorogenic probes, and a bright mitochondrial probe, working under live cell conditions. Harnessing the optical properties of a given fluorophore has been an important topic for a couple of decades, both in industry and in academia. This thesis provides useful insights for the improvement and development of unique small fluorescent materials, or optical materials.
Download or read book Design and Synthesis of Novel Donor acceptor donor Xanthene based Dyes from Heteronuclear Ring Systems for Chemical Electrochemical and Biological Sensory Materials written by Ishanka Nirmani Rajapaksha and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conventional xanthene dyes (eg: fluorescein and rhodamine) have their absorptions and emissions in the visible region, which limits their use in cellular imaging. Absorptions and emissions at longer wavelengths allow for low background cellular autofluorescence, deep tissue penetration, and minimum cell damage. Chapter I discusses the background of fluorescent dyes and the importance of near-infrared (NIR) emissive dyes for biological applications. Chapter II is based on the design and synthesis of new xanthene-based NIR I dyes using simple and short synthetic routes. This study used pyrrole and indole as donor molecules and combined them to the xanthene core by the Suzuki cross-coupling reaction to prepare the new dyes. After the treatment with trifluoroacetic acid, these new dyes transformed from their non-fluorescent to fluorescent forms and exhibited excellent red shifts in their maximum absorption and emission wavelengths. The novel pyrrole-based xanthene dye was used to investigate the efficacy of the dye as a probe for fluoride ions. We were able to modify this dye with a silyl ester receptor and develop a probe as a colorimetric turn-off fluoride ion sensor. In chapter III, we describe the synthesis of different NIR emissive xanthene dyes using the donor-acceptor-donor concept. New xanthene-based dyes were designed with five-membered heterocycles and fused heteronuclear molecules. Additionally, xanthene-based dyes containing an alkyne spacer were synthesized using the D-pi-A model to extend the pi-conjugation through the alkyne spacer. All of the dyes exhibited absorption and emission maxima in the visible to NIR I region, between 500-850 nm. In chapter IV, we discussed the synthesis of xanthene-based electrochromic materials. These compounds used xanthene as the chromophore and ferrocene as the electrophore units. Novel rhodamine-based symmetric and unsymmetric dyes were synthesized by attaching the ferrocene unit through the lactam ring. The compounds were then investigated as an electrochromic probe using UV-Vis, cyclic voltammetry, and spectroelectrochemical analysis.
Download or read book Synthesis Characterisation and Spectroscopic Analysis of Fluorescent Dyes for Applications based Chemistry written by Heather Fay Higginbotham and published by . This book was released on 2015 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: This research project investigates the synthesis and spectroscopic analysis of organic and inorganic fluorescent and luminescent materials for future use in applications-based chemistry. This work specifically focuses upon fluorescent dyes with tunable emission properties designed for the investigation of applications less commonly explored in literature. The use of advanced spectroscopic and single particle fluorescence techniques is also an underlying theme of each chapter, used to elucidate the mechanism of emissive output from synthesised materials.Initial research focused upon the development water-soluble naphthalene diimides for use in biophysical applications (Chapter 3). Quenching ratios in water were first probed using steady state and time-resolved fluorescence techniques revealing that both static and dynamic quenching mechanisms play a role in visible fluorescence emission. Encapsulation of fluorescent naphthalene diimides into reverse and liposomal micelles (both used as biological membrane mimics) highlighted their potential for biophysical applications. It was shown using single particle techniques that the cavity size of dye loaded reverse micelles and diffusional parameters and hydrodynamic radii of dye loaded liposomal micelles could be accurately determined. Further research using naphthalene diimides led to the development of a series of supramolecular host-guest materials used to investigate non-bonding interactions (Chapter 4). Small naphthalene diimides were synthesised and the change in their photophysical properties probed upon incorporation into a cavity molecule, cucurbit[8]uril, which served as host. Results showed that the non-bonding interactions between naphthalene diimides and cucurbit[8]uril could be probed using numerous steady state and time-resolved fluorescence techniques, with the most interesting of the complexes forming an emissive 'excimer like' species with a fluorescence quantum yield of 7% in water, and a Stokes shift of more than 100 nm. Core-substituted naphthalene diimides were further developed as fluorescent sensing materials for small analytes such as protons as well as redox active compounds (Chapter 5). Two proton sensing naphthalene diimides and a series of redox sensing derivatives were synthesised and the mechanism of the sensing event spectroscopically probed using both steady state and time-resolved spectroscopic techniques. The mechanism of proton sensing was found to be photoinduced electron transfer from an electron donating tertiary nitrogen attached to the naphthalene diimide, which is subsequently suppressed upon protonation leading to an increase in emission. The emission output from one of the proton sensing materials was also found to be highly dependent upon solvent polarity and time-resolved methods were used to elucidate that the closeness in energy between the singly excited and the charge separated state leads to delayed fluorescence. Redox sensitive naphthalene diimides were analysed using steady state, cyclic voltammetry and computational modeling revealing the presence of highly conjugated small molecule systems that absorb and emit in the red/deep red region of the electromagnetic spectrum. This emission was modulated by the addition of oxidants and reductants and switched the fluorescence output 'on' and 'off' many times.Studies at the single molecule level were also completed using CdSe quantum nanocrystals (Chapter 6). Taking advantage of the inherent photostability of these semiconducting materials, the emission dipoles of quantum nanocrystals of different sizes and shapes were probed using defocused wide-field microscopy. Comparison of emission patterns to theoretically determined patterns showed that unlike CdSe spheres, which have a no discreet emission dipole, CdSe rods contain a single dipole moment down the c-axis of the crystal. This discreet dipole emission however, appeared to breakdown in rods with very small aspect ratios behaving more like spheres again.
