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, making the film panchromatic . 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 2 sub N sup sup CH CH CH ... 960115293&dok var d1&dok ext pdf&filename 960115293.pdf Cyanine Direkte Funktionalisierung, Oligomerisierung ... chain. ref name ernst cite journal author Ernst LA, Gupta RK, Mujumdar RB, Waggoner AS title Cyanine ... water soluble fluorescent dyes of the cyanine dye family. Cy3 dyes fluoresce yellow green ... technical f cy3 5.asp author Jackson ImmunoResearch title Cyanine Dyes Cy2, Cy3, and Cy5 work accessdate ... R.B. Mujumdar, L.A. Ernst, S.R. Mujumdar, C.J. Lewis, A.S. Waggoner, Cyanine dye labeling reagents ... 2 Category Cyanine dyes Category Quaternary ammonium compounds de Cyanine fr Cyanine ja sv Cyaniner ... 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
File Diethyl cyanine.svg thumb 1,1 diethyl 2,2 cyanine chloride pseudoisocyanine chloride, PIC chloride A J aggregate is a type of dye with an absorption band that shifts to a longer wavelength bathochromic shift of increasing sharpness higher absorption coefficient when it aggregates under the influence of a solvent or additive or concentration as a result of supramolecular self organisation. ref W rthner, F., Kaiser, T. E. and Saha M ller, C. R. 2011 , J Aggregates From Serendipitous Discovery to Supramolecular Engineering of Functional Dye Materials . Angewandte Chemie International Edition, 50 3376 3410. doi 10.1002 anie.201002307 ref The dye can be characterized further by a small Stokes shift with a narrow band. The J in J aggregate refers to E.E. Jelley who discovered the phenomenon in 1936 ref Spectral Absorption and Fluorescence of Dyes in the Molecular State EDWIN E. JELLEY Nature 138, 1009 1010 12 December 1936 doi 10.1038 1381009a0 ref ref Nature 139, 631 10 April 1937 doi 10.1038 139631b0 Molecular, Nematic and Crystal States of I I Diethyl Cyanine Chloride EDWIN E. JELLEY ref . The dye is also called a Scheibe aggregate after G. Scheibe who also independently published on this topic in 1937 ref Naturwissenschaften Volume 25, Number 5, 75, DOI 10.1007 BF01493278 Polymerisation und polymere Adsorption als Ursache neuartiger Absorptionsbanden von organischen Farbstoffen G. Scheibe, L. Kandler and H. Ecker ref ref ber die Ver nderlichkeit der Absorptionsspektren in L sungen und die Nebenvalenzen als ihre Ursache G. Scheibe Angewandte Chemie Volume 50, Issue 11, pages 212 219, 13. M rz 1937 ref . Scheibe and Jelley independently observed that in ethanol the dye PIC chloride has two broad absorption maxima at around 19,000 cm sup 1 sup and 20,500 cm sup 1 sup and that in water a third sharp absorption maximum appears at 17,500 cm sup 1 sup 571 nm . The intensity ... dyes in general, with cyanine s, merocyanine s, squaraine and perylene bisimide s. In H ... more details
Unreferenced date November 2006 Image Aminoallyl Uridine.svg 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
chembox verifiedrevid 383790272 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 J aggregate References reflist Category Fluorescent dyes Category Benzoxazoles Category Pyrimidines Category Lactams Category Sulfonates heterocyclic stub ja ... more details
CD. There are three basic formulations of dye used in CD Rs Cyanine dye CD Rs were the earliest ones ... green in color. The earlier models were very chemically unstable and this made cyanine based discs unsuitable ... like Taiyo Yuden use proprietary chemical additives 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 ... exposed to direct sunlight. Although the additives used have made cyanine more stable, it is still .... Unlike cyanine , phthalocyanine is more resistant to UV rays and CD Rs based on this dye show ... sensitive than cyanine to writing laser power calibration, meaning that the power level used by the writing ... hybrid variations of the dye formulations, such as Formazan by Kodak a hybrid of cyanine ... their unstable cyanine CD Rs in the past, so the formulation of a disc cannot be determined based purely ... more details
Related dyes Similar cyanine dyes SYBR Green II SYBR Gold YO Oxazole Yellow TO Thiazole Orange PG PicoGreen References reflist DEFAULTSORT Sybr Green I Category Staining dyes Category Cyanine dyes Category ... more details
dyes like cyaninecyanine dyes or after single channel arrays using biotin and labelled streptavin ... Cyanine dyes, such as Cy3 and Cy5 Protocol natural sciences Replication sample replication Molecular ... more details
orphan date January 2010 Chembox verifiedrevid 385867106 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
fluorophores are derivatives of rhodamine TRITC , coumarin , and cyanine . ref cite book author ... , Oregon green, eosin, Texas red, and Biosearch Technologies Cal Fluor dyes Cyanine derivatives cyanine, Indocyanine green indocarbocyanine , oxacarbocyanine , thiacarbocyanine , merocyanine , and Biosearch ... 600 DNA TOTO 1, TO PRO 1 509 533 Vital stain, TOTO Cyanine Dimer TO PRO Cyanine Monomer Thiazole Orange ... more details
, rhodamine , xanthene such as fluorescein , and cyanine dyes. Sulfonation makes Alexa Fluor dyes ... extent the newer cyanine series. ref cite journal author Berlier JE, Rothe A, Buller G, et al. title ... more details
chembox verifiedrevid 464378790 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 UNII Ref fdacite correct FDA UNII E66400VT9R ChEBI Ref ebicite correct EBI ChEBI 17362 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 237 C 760mm Hg, 108 110 C 11mm Hg Solubility Soluble pKb 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. Citation needed 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 quin ... 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 ultra fine grain ref Recent developments in Lippman photography , Jean Marc Fournier, Benjamin R. Alexander, et. al. Proc. SPIE 3358, 95 1998 http spiedigitallibrary.org proceedings resource 2 psisdg 3358 1 95 1?isAuthorized no ref 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 themsel ... more details
Panchromatic film is a type of black and white photographic film that is sensitive to all wavelength s of visible light . Description A panchromatic film produces a realistic reproduction of a scene as it appears to the human eye. Almost all modern photographic film is panchromatic, but some types are orthochromatic and are not sensitive to certain wavelengths of light. As naturally prepared, silver halide photographic emulsion emulsions are much more sensitive to blue and UV light than to green and red wavelengths. The German chemist Hermann W. Vogel found out how to extend the sensitivity into the green, and later the orange, by adding sensitising dyes to the emulsion. By the addition of erythrosine the emulsion could be made orthochromatic while some cyanine derivative chemistry derivatives confer sensitivity to the whole visible spectrum making it panchromatic. However, his technique was not extended to achieve a fully panchromatic film until the early 1900s, shortly after his death. Panchromatic stock for still photographic plates became available commercially in 1906. ref Ralph E. Jacobson et al. , http books.google.com books?id HHX4xB94vcMC The Manual of Photography Photographic and Digital Imaging , 9th ed., Focal Press, p. 208. ISBN 978 0240515748. ref But the switch from orthochromatic film was only gradual panchromatic plates cost two to three times as much, and had to be developed in darkness, unlike orthochromatic which, being insensitive to red, could be developed under a red light in the darkroom. ref Geo. F. Greenfield, http books.google.com books?id 7a8EAAAAYAAJ&pg RA1 PA460 Practical Panchromatism in the Studio , Wilson s Photographic Magazine , October 1912, p. 460 461. ref And the process that increased the film s sensitivity to yellow and red also made it oversensitive to blue and violet, requiring a yellow red lens filter to correct it, which in turn reduced the total amount of light and increased the necessary exposure time. ref http books.goo ... 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 showing intense fluorescence , 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 wikt 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 cite journal author Sprenger, H. E. & Ziegenbein, W. journal Angew. Chem. Int. Ed. volume 5 year 1966 page 894 title Condensation Products of Squaric Acid and Tertiary Aromatic Amines doi 10.1002 anie.196608941 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 methyl 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 cite journal author E. Terpetschnig and J.R. Lakowicz title Synthesis and characterization of asymmetrical squarains a novel class of cyanine dyes doi 10.1016 0143 7208 93 85016 S journal Dyes and ... more details
with cyanine 5 Cy5 red deoxy cytosine triphosphate while the methylated DNA, enriched after the immunoprecipitation step, is labeled with cyanine 3 Cy3 green . The labeled DNA samples are cohybridized ... more details
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