Cyanine Dyes with High Absorption Cross Section as Donor Chromophores in Energy Transfer Primers1

Hung, Su-Chun; Ju, Jingyue; Mathies, Richard A.; Glazer, Alexander N.

doi:10.1006/abio.1996.0477

Cited by 53 publications

(40 citation statements)

References 5 publications

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“…44 An important characteristic of the detection dye in this context is that the excitation maximum of the dye^nucleic acid complex should be close to an available laser wavelength. Stains used in CE include SYBR 1 Oxazine derivative JA242 80 Platinum coproporphyrin 81,82 Rhodamine derivatives MR200-1 and JA169 80 5-Carboxyrhodamine (RHD) 83 Rhodamine green 29 Carboxy-X-rhodamine (ROX) 59,75 Carboxytetramethylrhodamine (TAMRA) 59 Tetrachloro-6-carboxy uorescein (TET) 83 Texas Red …”

mentioning

confidence: 99%

Stains, labels and detection strategies for nucleic acids assays

Kricka

2002

Ann Clin Biochem

134

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Selected developments and trends in stains, labels and strategies for detecting and measuring nucleic acids (DNA, RNA) and related molecules [e.g. oligo(deoxy)-nucleotides, nucleic acid fragments and polymerase chain reaction products] are surveyed based on the literature in the nal decade of the 20th century (1991--2000). During this period, important families of cyanine dyes were developed for sensitive detection of double-stranded DNA, single-stranded DNA, and oligo(deoxy)nucleotides in gels and in solution, and families of energy transfer primers were produced for DNA sequencing applications. The continuing quest for improved labels for hybridization assays has produced a series of candidate labels including genes encoding enzymes, microparticles (e.g. quantum dots, nanocrystals, phosphors), and new examples of the uorophore (e.g. cyanine dyes) and enzyme class of labels (e.g. re y luciferase mutants). Label detection technologies for use in northern and southern blotting assays have focused on luminescent methods, particularly enhanced chemiluminescence for peroxidase labels and adamantyl 1,2-dioxetanes for alkaline phosphatase labels. Sets of labels have been selected to meet the demands of multicolour assays (e.g. four-colour sequencing and single nucleotide primer extension assays). Non-separation assay formats have emerged based on uorescence polarization, uorescence energy transfer (TaqMan TM , molecular beacons) and channelling principles. Microanalytical devices (microchips), highthroughput simultaneous test arrays (microarrays, gene chips), capillary electrophoretic analysis and dipstick devices have presented new challenges and requirements for nucleic acid detection, and uorescent methods currently dominate in many of these applications.

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confidence: 99%

Stains, labels and detection strategies for nucleic acids assays

Kricka

2002

Ann Clin Biochem

134

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“…The synthesis of Cy2b was performed as described by Hung et al (15). The methods for the synthesis of Cy3 and Cy5 were derived from procedures published by Jung and Kim (16), Mader et al (17), and Mujumdar et al (18).…”

Section: Synthesis Of the Cyanine Dyesmentioning

confidence: 99%

Differential activity-based gel electrophoresis for comparative analysis of lipolytic and esterolytic activities

Morak

Schmidinger

Krempl

et al. 2009

Journal of Lipid Research

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We established a novel technique for differential activity-based gel electrophoresis (DABGE) of lipolytic enzymes from two different biological samples. For this purpose, a set of three fluorescent suicide inhibitors was developed. These probes possess the same substrate analogous structures but carry different cyanine dyes (Cy2b, Cy3, and Cy5) as reporter fluorophores. For comparison of enzyme profiles, two samples are individually labeled with a different probe followed by mixing, gel electrophoresis, fluorescence imaging, and identification of the tagged proteins by MS/MS. Protocols for quantitative determination of active enzymes were developed on the basis of lipolytic proteomes that had been admixed with defined amounts of known lipases and esterases. A detailed analysis of the fluorescence intensities showed that the found enzyme ratios very closely reflected the relative amounts of the labeled enzymes that were used for spiking. The DABGE method was used to compare the lipolytic proteomes of brown and white adipose tissue showing specific enzyme patterns of both samples. This study represents the first application of this technology for comparative analysis of lipases and esterases. Further applications of this technique can be expected to provide entirely new information on lipid enzymology in health and disease with high precision.-Morak, M., H. Schmidinger, P. Krempl, G. Rechberger, M. Kollroser, R. Birner-Gruenberger, and A. Hermetter. Differential activity-based gel electrophoresis for comparative analysis of lipolytic and esterolytic activities. In the postgenomic era, researchers are now challenging the proteome with methods like two-dimensional gel electrophoresis or multidimensional chromatography followed by mass spectrometry and various other methods for abundance-based proteome profiling. However, the amount of proteins present at a certain state of the cell might not correlate with the enzyme activities responsible for the metabolic fluxes, cell management, and signal transduction. Therefore, elucidation of changes in protein activity is the ultimate goal of functional proteomics.Methods have been developed for specific detection of enzymes on the basis of their catalytic activities. For this purpose, activity recognition probes (ARPs) (1) or activitybased probes are used. Basically, an ARP is a molecule consisting of i) a recognition site targeting a certain enzyme species, ii) a properly positioned reactive site that forms a covalent bond with the target, and iii) a tag for visualization and/or isolation of the covalently bound target (2-4). Many reactive groups have been developed so far for identifying different types of enzyme activity, i.e., fluorophosphonates for serine hydrolases (5), p-nitrophenyl organophosphonates for lipases and esterases (3, 6), epoxides for cysteine proteases (7), and sulfonate esters for various enzyme classes (8, 9). Two-dimensional (2D) gel electrophoresis is a well-established technique for simultaneous separation and display of hundreds to thousan...

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“…They consisted of two dyes per primer, one being a common donor and other the acceptor dye. The common donor could be a fluorescein derivative (FAM) or a cyanine (Cy5) [64] at the 5©-end. The second dye, the discriminating one, was located about ten bases away, with the separation between the dyes optimized for ET efficiency and minimum electrophoretic mobility shifts.…”

Section: Fluorescent-dye Chemistrymentioning

confidence: 99%

DNA sequencing by capillary array electrophoresis and microfabricated array systems

Carrilho

2000

Electrophoresis

113

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To comply with the current needs for high‐speed DNA sequencing analysis, several instruments and innovative technologies have been introduced by several groups in recent years. This review article discusses and compares the issues regarding high‐throughput DNA sequencing by electrophoretic methods in miniaturized systems, such as capillaries, capillary arrays, and microchannels. Initially, general features of several capillary array designs (including commercial ones) will be considered, followed by similar analyses with microfabricated array electrophoretic devices and how they can contribute to the success of large sequencing projects.

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Cyanine Dyes with High Absorption Cross Section as Donor Chromophores in Energy Transfer Primers1

Cited by 53 publications

References 5 publications

Stains, labels and detection strategies for nucleic acids assays

Stains, labels and detection strategies for nucleic acids assays

Differential activity-based gel electrophoresis for comparative analysis of lipolytic and esterolytic activities

DNA sequencing by capillary array electrophoresis and microfabricated array systems

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