Cyanine Dye Properties

The ability of cyanines to bind to DNA has led to the development of numerous fluorescence detection methods, mostly involving dyes that exhibit significant enhancements in fluorescence quantum yield upon binding. Covalent attachment of cyanines to DNA results in fluorescent labeling of the DNA, useful for a variety of applications including gene chip analysis and single molecule spectroscopy. 

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Rye, H. S, Yue, S, Wemmer, D. E, Quesada, M. A, Haugland, R. P, Mathies, R. A. and Glazer, A. N. (1992). Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes -Properties and applications. Nucleic Acids Res. 20, 2803-2812. 

Stable fluraescent complexes of double-stranded DNA with bisintercalating asymmetric cyanine dyes Properties and applications. Nucleic Acids Res., 20(11) 2803-2812. 

In the first chapter, devoted to thiazole itself, specific emphasis has been given to the structure and mechanistic aspects of the reactivity of the molecule most of the theoretical methods and physical techniques available to date have been applied in the study of thiazole and its derivatives, and the results are discussed in detail The chapter devoted to methods of synthesis is especially detailed and traces the way for the preparation of any monocyclic thiazole derivative. Three chapters concern the non-tautomeric functional derivatives, and two are devoted to amino-, hydroxy- and mercaptothiazoles these chapters constitute the core of the book. All discussion of chemical properties is complemented by tables in which all the known derivatives are inventoried and characterized by their usual physical properties. This information should be of particular value to organic chemists in identifying natural or Synthetic thiazoles. Two brief chapters concern mesoionic thiazoles and selenazoles. Finally, an important chapter is devoted to cyanine dyes derived from thiazolium salts, completing some classical reviews on the subject and discussing recent developments in the studies of the reaction mechanisms involved in their synthesis. 

Chapters III to VII discuss the general properties of thiazoles having hydrocarbon and functional substituents, respectively. A special chapter (Chapter VIII) is devoted to mcso-ionic thiazoles, and Chapter IX describes the thiazolium salts and their numerous cyanine dyes derivatives. The last chapter concerns the monocyclic selenazoles. 

The color and constitution of cyanine dyes may be understood through detailed consideration of their component parts, ie, chromophoric systems, terminal groups, and solvent sensitivity of the dyes. Resonance theories have been developed to accommodate significant trends very successfully. For an experienced dye chemist, these are useful in the design of dyes with a specified color, band shape, or solvent sensitivity. More recendy, quantitative values for reversible oxidation—reduction potentials have allowed more complete correlation of these dye properties with organic substituent constants. 

Excited-state properties of the cyanine and related dyes are complex. Most cyanine dyes exhibit small Stokes shifts for duorescence maxima. Typical carbocyanines (1) with n = 1 show 14- to 16-nm shifts in methanol solution with low quantum efficiencies for duorescence (Op ) of less than 0.05. The diearbocyanine analogues also show small Stokes shifts but higher quantum yields (Lpj = 0.3-0.5). 

A wide variety of stmetures exist in the cyanine, merocyanine, and oxonol classes of dyes. Properties that may affect toxicity vary widely also. These include solubihty, propensity to be oxidized or reduced, aggregation tendency, and diffusion through membranes. Specific acute toxicity data are Hsted in Table 2, and the LD q data vary widely with the test used. 

Neady every significant class of dyes and pigments has some members that function as sensitizers. Toxicological data are often included in surveys of dyes (84), reviews of toxic substance identification programs (85), and in material safety data sheets provided by manufacturers of dyes. More specific data about toxicological properties of sensitizing dyes are contained in the Engchpedia under the specific dye classes (see Cyanine dyes Polymethine dyes Xanthene dyes). 

The 2-methyl-4,9-dioxo-4,9-dihydrothiazolo[4,5-.g]quinoline was first quar-temized with methyl iodide on pyridine nitrogen and then treated with IV-methyl-quinolinium-4-yl salt, affording monomethine cyanine dyes 41 to study solva-tochromism, acid-base properties, and antimicrobial activities (95MI1). 

Cyanine Dyes Derived from Thiazolium Salts 1. Electrophilic Properties of Thiazolium Salts... 

Luschtinetz F, Dosche C, Kumke MU (2009) Influence of streptavidin on the absorption and fluorescence properties of cyanine dyes. Bioconjugate Chem 20 576-582... 

Sato S, Tsunoda M, Suzuki M, Kutsuna M, Takido-uchi K, Shindo M, Mizuguchi H, Obara H, Ohya H (2009) Synthesis and spectral properties of polymethine-cyanine dye-nitroxide radical hybrid compounds for use as fluorescence probes to monitor reducing species and radicals. Spectrochim Acta A 71 2030-2039... 

Benson RC, Kues HA (1977) Absorption and fluorescence properties of cyanine dyes. J Chem Eng Data 22 379-383... 

Thomas, L, Netzel, K. N. and Zhao, M. (1995). Base-content dependence of emission enhancements, quantum yields, and lifetimes for cyanine dyes bound to double-strand DNA Photophysical properties of monomeric and bichromophoric DNA stains. J. Phys. Chem. 99,17936-17947. 

Most companies selling cyanine dyes do not reveal their exact structures. This likely is due to each company keeping proprietary the small synthetic tweaks that create unique fluorescence properties for their dyes. However, some structures are available through published documents, such as patents and early publications (Leung et al., 2005). Figure 9.45 illustrates some of these structures, which may not reflect precisely what any one company actually offers today, but it gives an idea of the types of modifications that can be done to add water solubility and reactivity. 

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