Image CyanineDye.gif right 300px An example cyanine dye. Cyanine is a International Union of Pure and Applied Chemistry nomenclature non systematic name of a synthetic dye family belonging to polymethine group. Cyanines have many uses as fluorescent dyes, particularly in biomedical imaging. Depending on the structure, they cover the spectrum from infrared IR to ultraviolet UV . Cyanines were originally used, and still are, to increase the sensitivity range of photo emulsion photographic emulsions , i.e., to increase the range of wavelength s which will form an image on the film. Cyanines are also used in CD R and DVD R media. The ones used are mostly green or light blue in color, and are chemically unstable. This makes unstabilized cyanine discs unsuitable for archival CD and DVD use, as they can fade and become unreadable in a few years, however, recent cyanine discs contain stabilizers that slow down the deterioration significantly. These discs are often rated with an archival life of 75 years or more. The other dyes used in CD Rs are phthalocyanine and Azo compound azo . Cyanines were first synthesized over a century ago, and there are a large number reported in the literature. Structure Image Cyanine.png thumb right 300px The Cyanines br I Streptocyanines, br II Hemicyanines, br III Closed cyanine There are three types of cyanines Streptocyanines or open chain cyanines R sub ... nb.de cgi bin dokserv?idn 960115293&dok var d1&dok ext pdf&filename 960115293.pdf Cyanine Direkte Funktionalisierung ..., Waggoner AS title Cyanine dye labeling reagents for sulfhydryl groups journal Cytometry volume 10 issue ... and Cy5 Cy3 and Cy5 are reactive water soluble fluorescent dyes of the cyanine dye family. Cy3 dyes ... f cy3 5.asp author Jackson ImmunoResearch title Cyanine Dyes Cy2, Cy3, and Cy5 work accessdate ... Mujumdar, C.J. Lewis, A.S. Waggoner, Cyanine dye labeling reagents sulfoindocyanine succinimidyl esters ... reflist 2 Category Cyanine dyes Category Quaternary ammonium compounds de Cyanine fr Cyanine ja ... more details
DII may refer to Days in inventory , an accounting term Dii , the Thracian tribe DiI , a hydrophobic cyanine dye used in cell biology Delegation of the Ismaili Imamat , the Delegation of the Ismaili Imamat Diablo II , a sequel to the computer game Diablo Division II NCAA Division II , a competition level in the National Collegiate Athletic Association NCAA Defence Information Infrastructure , the UK s secure military communications network Dynamic Invocation Interface , part of the CORBA standard DII may also mean 502 in Roman numerals disambig de DII eo DII it DII ... more details
unreferenced date December 2010 orphan date January 2010 Image P19 cell sorting out.png thumb right 228px Cultured embryonal carcinoma were stained with either DiI red or DiO green . The image was captured by scanning confocal microscopy. DiI is a hydrophobic and lipophilic cyanine dye used for scientific purposes, such as Single molecule experiment single molecule imaging , Fate mapping , and neuronal tracing as it is retained in the lipid bilayers . Its chemical name is 1,1 dioctadecyl 3,3,3 3 tetramethylindocarbocyanine perchlorate, the chemical formula is C sub 59 sub H sub 89 sub ClN sub 2 sub O sub 4 sub Category Fluorescence Category Staining dyes chem stub ... more details
Unreferenced date November 2006 Image Aminoallyl Uridine.gif right frame The structure of aminoallyluridine Aminoallyl nucleotides are used in post labeling of nucleic acid s to be used in microarray s. These nucleotides are formally known as 5 3 amino allyl nucleotides since the aminoallyl group is usually attached to carbon 5 of the pyrimidine ring of uracil and cytosine . They are usually abbreviated as aa , such as aa dUTP. The amine group in the aminoallyl moiety is aliphatic and thus more reactive compared to the amine groups that are directly attached to the rings aromatic of the bases. Uses The aminoallyl group in aminoallyl modified nucleotides is reactive with dyes such as the cyanine series, AnaSpec HiLyte Fluor , or Alexa Fluor dyes that also been modified to be amine reactive. A problem with this method is that the dyes react with the buffering agent usually used for storage of nucleotides. Instead a carbonate buffer is used. The DNA or RNA from a sample is copied in vitro by T7 polymerase, RT polymerase or some other polymerase except of eukaryotic origin in a mix of nucleotides in which one, typically uracil RNA and also DNA , is a mix aminoallyl NTP and normal UTP. An alternative method is using thiol reactive dyes. DEFAULTSORT Aminoallyl Nucleotide Category Nucleic acids Category Nucleotides molecular cell biology stub ... more details
used in CD Rs Cyanine dye CD Rs were the earliest ones developed, and their formulation is patent ... chemically unstable and this made cyanine based discs unsuitable for archival use they could fade ... to make more stable cyanine discs metal stabilized Cyanine , Super Cyanine . Older cyanine dye based CD Rs, as well as all the hybrid dyes based on cyanine, were very sensitive to UV rays and could ... the additives used have made cyanine more stable, it is still the most sensitive of the dyes in UV ... on this are often given a rated lifetime of hundreds of years. Unlike cyanine , phthalocyanine is more ... of direct sunlight exposure. However, phthalocyanine is more sensitive than cyanine to writing laser ... formulations, such as Formazan by Kodak a hybrid of cyanine and phthalocyanine . Unfortunately, many manufacturers have added additional coloring to disguise their unstable cyanine CD Rs in the past, so ... more details
dyes like cyaninecyanine dyes or after single channel arrays using biotin and labelled streptavin ... Quantification of nucleic acids Cyanine dyes, such as Cy3 and Cy5 Protocol natural sciences Replication ... more details
orphan date January 2010 Chembox Reference ref http www.sigmaaldrich.com catalog ProductDetail.do?lang en&N4 318426 ALDRICH&N5 SEARCH CONCAT PNO BRAND KEY&F SPEC 3,3 Dihexyloxacarbocyanine iodide at Sigma Aldrich ref ImageFile dihexyloxacarbocyanine iodide.png ImageSize 200px IUPACName 3 Hexyl 2 3 3 hexyl 2 3 H benzoxazolylidene 1 propenyl benzoxazolium iodide OtherNames 3,3 Dihexyloxacarbocyanine iodide Section1 Chembox Identifiers CASNo 53213 82 4 PubChem 9894321 SMILES CCCCCCN 1C2 CC CC C2O C1 C C C C3 N C4 CC CC C4O3 CCCCCC. I Section2 Chembox Properties C 29 H 37 I 1 N 2 O 2 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition DiOC sub 6 sub 3,3 dihexyloxacarbocyanine iodide is a fluorescent dye used for the staining of a cell s endoplasmic reticulum , ref cite journal author Terasaki M. title Fluorescent labeling of endoplasmic reticulum journal Methods Cell Biol. year 1989 volume 29 pages 125 35 pmid 2643757 ref vesicle membranes and mitochondria . ref cite journal author Koning AJ et al. title DiOC6 staining reveals organelle structure and dynamics in living yeast cells journal Cell Motil Cytoskeleton year 1993 volume 25 issue 2 pages 111 28 doi 10.1002 cm.970250202 pmid 7686821 ref Binding to these structures occurs via the dye s hydrophilic groups. DiOC sub 6 sub can be used to label living cells, however they are quickly damaged due to phototoxicity photodynamic toxicity , so cells stained with this dye can only be exposed to light for short periods of time. When exposed to blue light, the dye fluorescence fluoresces green. References reflist Category Fluorescent dyes Category Cyanine dyes Category Vital stains Category Benzoxazoles Category iodides Category Quaternary ammonium compounds Organic compound stub ... more details
chembox Name Merocyanine I ImageFile Merocyanine.png ImageSize 200px IUPACName sodium 3 2 Z 2 E 4 1,3 Dibutyl 2,4,6 trioxo 5 hexahydropyrimidinylidene but 2 enylidene 1,3 benzoxazol 3 yl propane 1 sulfonate OtherNames Section1 Chembox Identifiers CASNo 58823 12 4 PubChem 23678802 SMILES CCCCN1C O C CC CC C2N C3 CC CC C3O2 CCCS O O O C O N C1 O CCCC. Na Section2 Chembox Properties Formula C sub 26 sub H sub 32 sub N sub 3 sub NaO sub 7 sub S MolarMass 553.60 g mol Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Merocyanines are a class of fluorescent dye s typified by merocycanine I. These dyes are usually intensely colored and have large Opacity optics Extinction coefficient extinction coefficients . Merocyanine 540 was the first fluorescent dye used for measuring membrane potential ref http www.anaspec.com products product.asp?id 29835 Merocyanine 540 ref , while Brooker s merocyanine and related compounds are notable for their Solvatochromism solvatochromatic properties. Image Merocyanine 540.png thumb left Merocyanine 540 br style clear left See also cyanine References reflist Category Fluorescent dyes Category Benzoxazoles Category Pyrimidines Category Lactams Category Sulfonates heterocyclic stub ja ... more details
Cal Fluor dyes Cyanine derivatives cyanine, Indocyanine green indocarbocyanine , oxacarbocyanine ... 503 530 640 DNA RNA SYTOX Green 504 523 600 DNA TOTO 1, TO PRO 1 509 533 Vital stain, TOTO Cyanine Dimer TO PRO Cyanine Monomer Thiazole Orange 510 530 Propidium Iodide PI 536 617 668.4 LDS 751 543 590 ... more details
sulfonate sulfonation of coumarin , rhodamine , xanthene such as fluorescein , and cyanine dyes ... 002215549904700910 ref and to some extent the newer cyanine series. ref cite journal author Berlier ... more details
chembox verifiedrevid 414044219 ImageFile Quinoline chemical structure part1.png ImageSize 200px ImageFile1 Quinoline chemical structure part2.png ImageSize1 200px IUPACName Quinoline OtherNames 1 benzazine, 1 azanaphthalene, benzo b pyridine Section1 Chembox Identifiers ChemSpiderID Ref chemspidercite correct chemspider ChemSpiderID 6780 KEGG Ref keggcite correct kegg KEGG C06413 InChI 1 C9H7N c1 2 6 9 8 4 1 5 3 7 10 9 h1 7H InChIKey SMWDFEZZVXVKRB UHFFFAOYAU ChEMBL Ref ebicite correct EBI ChEMBL 14474 StdInChI Ref stdinchicite correct chemspider StdInChI 1S C9H7N c1 2 6 9 8 4 1 5 3 7 10 9 h1 7H StdInChIKey Ref stdinchicite correct chemspider StdInChIKey SMWDFEZZVXVKRB UHFFFAOYSA N CASNo 91 22 5 CASNo Ref cascite correct CAS PubChem 7047 SMILES n1cccc2ccccc12 Section2 Chembox Properties Formula C sub 9 sub H sub 7 sub N MolarMass 129.16 g mol Appearance Density 1.093 g ml MeltingPt &minus 15 C BoilingPt 108 110 C 11mm Hg Solubility Soluble pKa 4.85 ref Brown, H.C., et al., in Baude, E.A. and Nachod, F.C., Determination of Organic Structures by Physical Methods , Academic Press, New York, 1955. ref Quinoline is a heterocyclic aromatic organic compound . It has the formula C sub 9 sub H sub 7 sub N and is a colourless hygroscopic liquid with a strong odour. Aged samples, if exposed to light, become yellow and later brown. Quinoline is only slightly soluble in cold water but dissolves readily in hot water and most organic solvents. Quinoline is mainly used as a building block to other specialty chemicals. Approximately 4 tonne s are produced annually according to a report published in 2005. Fact date February 2008 Its principal use is as a precursor to 8 hydroxyquinoline , which is a versatile chelating agent and precursor to pesticides. Its quinaldine 2 and lepidine 4 methyl derivatives are precursors to cyanine dye s. Oxidation of quinoline affords quinolinic acid pyridine 2,3 dicarboxylic acid , a precursor to the herbicide sold under the name Assert . ref name Hok ... more details
Image Lippmann photo view.jpg thumb Early colour photograph by Lippmann Gabriel Lippmann conceived a two step method to record and reproduce colours, known as direct photochromy photochromes , ref name Eder668,670 672 cite book last Eder first J.M authorlink coauthors title History of Photography, 4th. edition trans title Geschichte der Photographie year 1945 origyear 1932 publisher Dover Publications, Inc. location New York pages 668, 670, 671, 672 url doi id isbn 0486235866 ref interference photochromes , ref name Eder668,670 672 Lippmann photochromes , ref name Eder668,670 672 Photography in natural colours by direct exposure in the camera ref name Eder668,670 672 Lippmann process of colour photography . ref patent US 6556992 ref A Lippmann plate is a clear glass plate having no Anti halation backing , coated with an almost transparent very low silver halide content emulsion of extremely fine grains, typically 0.01 to 0.04 micrometres in diameter. ref R.W.G. Hunt, The Reproduction of Colour , 6th ed, p6 ref Consequently, Lippmann plates have an extremely high http www.tpub.com content photography 14209 css 14209 56.htm resolving power exceeding 400 lines mm. Method In Lippmann s method a glass plate was coated with a grainless as fine grained as possible colour sensitive film using the Abel Niepce de Saint Victor Albumen Process containing potassium bromide, dried, sensitized in the silver bath, washed, flowed with cyanine solution, dried and then brought into optical contact with a reflection surface the back of the plate is then flowed in a plate holder of special form with pure mercury element mercury and exposed in the camera through the glass side of the plate, so that the light rays which strike the transparent light sensitive film, are reflected in themselves and create interference phenomena of Standing wave stationary waves . ref name Eder668,670 672 The standing waves cause exposure of the emulsion in diffraction patterns. The developed and fixated diff ... more details
File Squarainedyes.png thumb 380px top a 1,2,3,3 tetramethyl 3H indolium salt and bottom aniline derivative of Squaraine Dyes Squaraine Dyes are a class of organic dyes with very intense fluorescence spectra, typically in the red and near infrared region Absorption maxima are found between 630 and 670 nm and their emission maxima are between 650 700 nm . They are characterized by their unique aromatic four membered ring system derived from squaric acid . Most squaraines are encumbered by nucleophilic attack of the central four membered ring, which is highly electron deficient . This encumbrance can be attenuated by the formation of a rotaxane around the dye to protect it from nucleophiles. They are currently used as sensors for ions and have recently, with the advent of protected squanaine derivatives, been exploited in biomedical imaging. Synthesis Synthesis of squaraine dyes was reported at least in 1966 ref Sprenger, H. E. & Ziegenbein, W., Angew. Chem. Int. Ed. Engl., 5 1966 894 ref . They are derived from squaric acid which undergoes an electrophilic aromatic substitution reaction with an aniline or another electron rich derivative to form a highly conjugated product with extensive charge distribution. For instance, squaraine dyes are also formed via reaction of squaric acid or its derivatives with so called methylene bases like 2 methyl indolenines, 2 metyl benzthiazoles or 2 methyl benzo selenazoles. Indolenine based squaraines combine good photostability including high quantum yields when bound to proteins and reactive versions of these dyes are commonly used as fluorescent probes and labels for biomedical applications ref E. Terpetschnig and J.R. Lakowicz, Synthesis and characterization of asymmetrical squarains a novel class of cyanine dyes http dx.doi.org 10.1016 0143 7208 93 85016 S Dyes and Pigments 21, 227 234 1993 ref ref E. Terpetschnig et al. An investigation of squaraines as a new class of fluorophores with long wavelength excitation and ... more details
DNA microarray A fraction of the input DNA obtained after the sonication step above is labeled with cyanine ... step, is labeled with cyanine 3 Cy3 green . The labeled DNA samples are cohybridized ... more details
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