Fluorescence reporter dye

Fig. 20.18. The template (L-phenylalanine amide) and the fluorescent reporter dye used in this study. The other reporters examined (dansyl L-phenylalanine and 4-nitrophenol) were unsuccessful.

Hydrolysis probes (e.g.,TaqMan probes) are the most widely used and pubhshed in detection chemistry hterature for probe-based real-time PCR apphcations. In addition to the primers, it includes a third oligonucleotide, 20 to 26 bases in length, in the reaction known as the probe. A fluorescent reporter dye, most frequendy... 

The use of a sequence specific fluorescent probe The fluorescent probe (IT ) hybridizes to the target sequence after the denaturation step. The probe uses fluorescent resonance energy transfer technology, whereby the emission spectrum of a fluorescent reporter dye at its 5 end is effectively quenched by a second fluorescent dye at its 3 end when the probe is intact. The fluorescent signal is prodnced during primer extension when the 5 end is displaced by the amplicon and being cleaved by the nick specific 5 nuclease. 

Karuso, P. H. Choi, H. Y. Determination of the activity of a hydrolase or other hydrolytic agent and real-time monitoring of biomolecule digestion using a fluorescent reporter dye. PCT Int. Appl. WO 2007051257,2007 Chem. Abstr. 2007,146,477766. 

B. Simultaneous use of multiple fluorescent reporter dyes for glucose sensing in aqueous solution. Anal. Bioanal. Chem. 2007,387, 2767-2773. 

Real-time PCR is a quantitative method for measuring amplicons as they are produced by measuring the increase in fluorescence of a dye added to the reaction mixture.12,104,105 Methods using fluorescent reporters, such as SYBR Green,104,106 TaqMan ,107,108 or molecular beacons,9 collect quantitative data at the time when DNA is in the exponential phase of amplification. 

The formation of complexes of the fluorescent tracer dye ammonium 1-phenyl-aminonaphthalene-8-sulphonate (10.41) with cyclodextrins has been investigated with favourable results, especially in environmental studies [33]. The ability of this dye to complex with cyclodextrins has been exploited mainly as an analytical tool in the study of cyclodextrin applications, since its fluorescence is easily measured. The interaction of a-, P-and y-cyclodextrins with azo acid dyes containing alkyl chains of different lengths has been reported [36,37]. The formation and isolation of solid complexes between P-cyclodextrin and Cl Acid Red 42, Cl Acid Blue 40 or Erionyl Bordeaux 5BLF (Ciba) have been reported [29]. 

Simultaneous application of two emitting reporters allows providing the self-referenced reporter signal based on simple intensity measurements, without application of anisotropy or lifetime sensing that impose stringent requirements on fluorescence reporters. Usually, the two dyes are excited at a single wavelength with the absence or in the presence of interaction between them. 

There are many possibilities to use these complex formations in fluorescence sensing. If the excimer is not formed, we observe emission of the monomer only, and upon its formation there appears characteristic emission of the excimer. We just need to make a sensor, in which its free and target-bound forms differ in the ability of reporter dye to form excimers and the fluorescence spectra will report on the sensing event. Since we will observe transition between two spectroscopic forms, the analyte binding will result in increase in intensity of one of the forms and decrease of the other form with the observation of isoemissive point [22]. 

Callis PR (2010) Electrochromism and solvatochromism in fluorescence response of organic dyes. A nanoscopic view. In Demchenko AP (ed) Advanced Fluorescence Reporters in Chemistry and Biology I. Springer Ser Fluoresc 8 309-330... 

This comparison of the spectroscopic properties of the different types of fluorescent reporters underlines that semiconductor QDs and upconverting nanoparticles have no analogs in the field of organic dyes. Therefore, their unique features are unrivaled. The different molecular labels detailed here each display unique advantages that can compete with some of the favorable features of QDs and upconverting phosphors such as long lifetimes in the case of MLC systems and lanthanide chelates or very narrow emission bands for lanthanide chelates beneficial for spectral multiplexing. 

Pu KY, Liu B (2010) Fluorescence reporting based on FRET between conjugated polyelectrolyte and organic dye for biosensor applications. In Demchenko AP (ed) Advanced fluorescence reporters in chemistry and biology. II. Springer Ser Fluoresc 8 417 -53... 

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