Resonance energy transfer hybridization

Okamura, Y. and Watanabe, Y. (2006). Detecting RNA/DNA hybridization using double-labeled donor probes with enhanced fluorescence resonance energy transfer signals. Methods Mol. Biol. 335, 43-56. 

The sensor for the measurement of high levels of CO2 in gas phase was developed, as well90. It was based on fluorescence resonance energy transfer between 0 long-lifetime ruthenium polypyridyl complex and the pH-active disazo dye Sudan III. The donor luminophore and the acceptor dye were both immobilized in a hydrophobic silica sol-gel/ethyl cellulose hybrid matrix. The sensor exhibited a fast and reversible response to carbon dioxide over a wide range of concentrations. 

Goldman ER, Medintz IL, Whitley JL et al (2005) A hybrid quantum dot-antibody fragment fluorescence resonance energy transfer-based TNT sensor. J Am Chem Soc 127 6744-6751... 

Henry MR, Wilkins Stevens P, Sun J, Kelso DM (1999) Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer. Anal Biochem 276 204-214... 

The intersubunit rotation is required for translocation as ribosomes trapped in the nonrotated state by an engineered intersubunit disulfide bridge fail in tRNA-mRNA movement. Real-time observation of intersubunit movement by fluorescence resonance energy transfer (FRET) showed that intersubunit movement occurs concomitantly with hybrid state formation, and that the rotated state can be trapped by the antibiotic viomycin. Similarly to the fluctuation of tRNAs between classical and hybrid states, single-molecule studies have detected spontaneous intersubunit movement where the 3 OS subunit fluctuates between a rotated... 

Goldman, E. R., I. L. Medintz, J. L. Whitley, A. Hayhurst, A. R. Clapp, H. T. Uyeda, J. R. Deschamps, M. E. Lassman, and H. Mattoussi. A hybrid quantum dot-antibody fragment fluorescence resonance energy transfer-based TNT sensor. J. Am. Chem. Soc. 127, 6744-6751 (2005b). 

Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE. Detection of nucleic acid hybridization by non-radiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. U.S.A. 36. 1988 85 8790-8794. 

A third application for fluorescent PNA probes is to introduce fluorescent labels into the RNA site specifically (20). For example, PNA probes have been hybridized at exonic sites that flank consecutive splice sites in a pre-mRNA from yeast. Fdrster resonance energy transfer (FRET) donor and acceptor dyes were attached covalently to the PNAs, and low FRET efficiencies were observed when the PNAs were hybridized to the pre-mRNA. However, when hybridized to the mRNA produced by splicing, large increases in ERET have been observed both in bulk solution and on a glass slide where single-molecule measurements could be made. As in the EISH applications, the ability to use short PNA probes to deliver the fluorescent dye to a desired location decreased the likelihood that the PNA wiU disrupt the structure and the function of the RNA that is under investigation. 

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.)...

Fluorescence increases by resonance energy transfer as probes hybridize to product... 

Homogeneous Solution Hybridization with Fluorescence Resonance Energy Transfer, 625... 

By covalent attachment of fluorescein (as donor) and rhodamine (as acceptor) to the 5 -termini of complementary oligodeoxyribonucleotides, hybridization can be measured by non-radiative fluorescence resonance energy transfer (FRET) from fluorescein to rhodamine as hybridization occurs, the emission intensity of fluorescein falls while that of rhodamine rises." 9 Correction must be made for... 

Current methods combine at least one of four different principles of allelic discrimination (hybridization, primer extension, ligation, or restriction) with one of four different detection techniques (chemiluminescence/ fluorescence, fluorescence polarization, resonance energy transfer, and mass spectrometry). Assay formats range from (slab)- gel electrophoresis, plates, particles, fibre arrays, and microchip arrays to semi- and homogenous assays that do not require any further sample separation or purification. 

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