Fluorescence resonance energy transfer quench

Fluorescence resonance energy transfer (quenched fluorescence, InVitroGen Z -LYTE)... 

Figure 10.3. Modified Jablonski diagram for the processes of absorption and fluorescence emission (left), dynamic quenching (middle), and fluorescence resonance energy transfer (FRET) (right).

Fluorescence resonance energy transfer (FRET) and fluorescence quenching for... 

While the capture on DNA chips of fluorophore-labelled targets, and the extension of arrayed primers with fluorophore-labelled nucleotides has been widely used for some time, it is only more recently that assay formats have developed that utilize immobilized nucleic acids already modified with fluorophores. Fundamental analyses of surface monolayer structures and chemistries can be readily performed by immobilizing such modified oligonucleotides into SAM structures [105,106], but it is those interactions that can be monitored using fluorescence quenching or fluorescence resonance energy transfer (FRET) that have gained the most attention. 

Chemically modified crowned spirobenzopyran 112, containing a pyrenyl fluorophore attached at the nitrogen atom, can function as a fluorescence emission switch <2004T6029>. This sensor displayed a quenching of the PET fluorescence emission of the fluorophore in the absence of metal ions (the merocyanine form was not produced). When, however, the spiro form of 112 was converted into the merocyanine form by metal ion complexation of the crown ether portion of the molecule, a fluorescence resonance energy transfer (FRET) from the pyrene to the merocyanine moiety took place, producing fluorescence emission. 

He L, Olson DP, Wu X, Karpova TS, McNally JG, Lipsky PE. A flow c)4ometric method to detect protein-protein interaction in living cells by directly visualizing donor fluorophore quenching during CFP-YFP Fluorescence Resonance Energy Transfer (FRET). Cytometry 2003 55A 71-85. 

Marras SA, Kramer FR, Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 2002 30 el22. 

Interactions between fluorophores and with other molecules are reflected in proeesses like fluorescence resonance energy transfer (FRET), quenching and excimer formation. These phenomena can be used to study lateral diffusion and... 

Figure 37-24 Common probes and dyes for real-time PCR. f/J Double-stranded DNA dyes show a significant increase in fluorescence when bound to DNA (hv = excitation light). (2) Adjacent hybridization probes. Fluorescence resonance energy transfer (FRET) is illustrated between a donor and acceptor fluorophore.The x indicates phosphorylation of the 3 terminus of the probe to prevent polymerase extension. (3) FRET between a labeled primer and a single hybridization probe. (4) Hydrolysis probes are cleaved between the reporter and quencher, resulting in increased fluorescence. (5) Hairpin probes are quenched in the native conformation, but increase in fluorescence when hybridized. (6) Hairpin primers retain their native, quenched conformation until they are incorporated into a double-stranded product (Modified with permission of the publisher from Pritham GH, Wittwer CT Continuous f/uorescent monitoring of PCR.J Clin Ug Assay 1998, 21 404-412. 1998 Clinical Ligand Assay Society, Inc.)...

The binding of synthetic ion channels and pores to lipid bilayer membranes often causes a change in intra- or intermolecular self-organization that is visible in sufficiently sensitive methods such as fluorescence (e.g. tryptophan emission) [14] or circular dichroism spectroscopy and can be used to determine the partition coefficient. Convenient methods of detection under relevant conditions are fluorescence resonance energy transfer (FRET) or fluorescence depth quenching (FDQ) [3, 4, 6]. Many fluorescent probes for the labeling of both synthetic ion channels/... 

An example of this technology is the HIV protease assay shown in Fig. 9, which was published by Wang and co-workers [67]. The peptide substrate is labeled at the amino terminus with EDANS (5-((2 -aminoethyl)amino)naphthalene-l-sulfonic acid) as a donor fluorophore and at the carboxyl terminus with DABCYL (4-((4 -(di-methylamino)phenyl)azo)benzoic acid) as the acceptor chromophore. In the intact peptide, fluorescence resonance energy transfer (FRET) from EDANS to DABCYL results in quenching of the EDANS fluorescence. On cleavage of the peptide by HIV protease, the fluorescence of EDANS is restored. 

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