Fluorescent probes energy transfer

Takakusa H, Kikuchi K, Urano Y, Kojima H, Nagano T (2003) A novel design method of ratiometric fluorescent probes based on fluorescence resonance energy transfer switching by spectral overlap integral. Chemistry 9 1479-1485... 

Hagiwara Y, Hasegawa T, Shoji A et al (2008) Acridone-tagged DNA as a new probe for DNA detection by fluorescence resonance energy transfer and for mismatch DNA recognition. Bioorg Med Chem 16 7013-7020... 

Sinev, M., Landsmann, P., Sineva, E., Ittah, V. and Haas, E. (2000). Design consideration and probes for fluorescence resonance energy transfer studies. Bioconjug. Chem. 11, 352-362. 

Grunewald, J., Kopp, F., Mahlert, C., Linne, U., Sieber, S. A. and Marahiel, M. A. (2005). Fluorescence resonance energy transfer as a probe of peptide cyclization catalyzed by nonribosomal thioesterase domains. Chem. Biol. 12, 873-881. 

Didenko, V. V. (2001). DNA probes using fluorescence resonance energy transfer (FRET) Designs and applications. Biotechniques 31,1106-1116. 

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. 

Dennis, A. M. and Bao, G. (2008). Quantum dot-fluorescent protein pairs as novel fluorescence resonance energy transfer probes. Nano Lett. 8, 1439-45. 

An increase in sensitivity and reliability of chip analysis can also be achieved by using fluorescence resonance energy transfer (FRET). For this purpose both the probe and the target are labeled with a fluorophor. When the emission spectrum of the donor, e.g. Cy5, overlaps with the absorption spectrum of the acceptor, e.g. Cy5.5, and the donor and the acceptor are at a certain distance from each other, energy is transferred from the donor to the acceptor on excitation of the donor fluorophor. 

The already critical need for molecular-scale compositional mapping will increase as more complex structures are assembled. Currently, electron microscopy, scanning probe microscopy (SPM) and fluorescence resonance energy transfer (FRET) are the only methods that routinely provide nanometer resolution. 

Fluorescence resonance energy transfer has also been used for ionic strength measurements.(95) Fluorescein labeled dextran (donor) and polyethyleneimine-Texas Red (acceptor) were placed behind a dialysis membrane. The polymer association is ionic strength dependent and the ratio of intensities (F o/Fw) was used as the measured parameter. Since both the donor and acceptor are fluorescent, this kind of sensor may allow expand the sensitive ionic strength range by shifts in observation wavelength, as was discussed for pH probe Carboxy SNAFL-2 (see Section 10.3). 

Fluorescence resonance energy transfer (FRET) occurs when the excited state energy is transferred from a donor (D) to an acceptor (A). In general, probes containing two separate molecules can be synthesized, a fluorophore (D) and an analyte-sensitive acceptor (A) as shown below ... 

Koo, K., and Jaykus, L.-A. (2003). Detection of Listeria monocytogenes from a model food by fluorescence resonance energy transfer-based PCR with an symmetric fluorogenic probe set. Appl. Environ. Microbiol. 69,1082-1088. 

The elucidation of the structure, dynamics and self assembly of biopolymers has been the subject of many experimental, theoretical and computational studies over the last several decades. [1, 2] More recently, powerful singlemolecule (SM) techniques have emerged which make it possible to explore those questions with an unprecedented level of detail. [3-55] SM fluorescence resonance energy transfer (FRET), [56-60] in particular, has been established as a unique probe of conformational structure and dynamics. [26-55] In those SM-FRET experiments, one measures the efficiency of energy transfer between a donor dye molecule and an acceptor dye molecule, which label specific sites of a macromolecule. The rate constant for FRET from donor to acceptor is assumed to be given by the Forster theory, namely [59,61-64]... 

Walter, N. G. (2003). Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET). Curr. Protoc. Nucleic Acid Chem. Chapter 11, Unit 11 10. 

Ha, T., Enderle, T., Ogletree, D. F., Chemla, D. S., Selvin, P. R., and Weiss, S. (1996). Probing the interaction between two single molecules Fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl. Acad. Sci. USA 93, 6264-6268. 

The fluorescence is quenched by collisional quenching and fluorescence resonance energy-transfer (FRET). When the probe sequence anneals to the target sequence fluorescence... 

Mahajan, N.P., Linder, K., Berry, G., Gordon, G.W., Heim, R. and Herman, B. (1998). Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer. Nature Biotechnology, 16, 547-552. 

More recently double stranded DNA-binding dyes, (e.g., SYBR Green), have been introduced (Giulietti et al. 2001) which removed the need for an expensive, specific probe to be designed. Other sophisticated tools have been developed to work in conjunction with the Taqman method, for example molecular beacons, scorpions and hybridisation probes. These techniques rely on the FRET (Fluorescence Resonance Energy Transfer) principle but do not require the nuclease activity of the Taq polymerase. The different real-time... 

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