Quencher, molecular beacon

Hwang GT, Seo YJ, Kim BH (2004) A Highly discriminating quencher-free molecular beacon for probing DNA. J Am Chem Soc 126 6528-6529... 

Fig. 14. Examples of homogeneous hybridization assay methods (F luminophore, Q quencher, D donor, A acceptor). Thick lines represent DNA strands. Open circles on DNA strands indicate a SNP/mutation site for Molecular Beacon and insertion/deletion sites for dual FRET probe and dual FRET Molecular Beacon when these methods are applied to SNP/mutation typing or deletion/insertion detection. The solid circle on die strand indicates the complementary site.

Tsourkas et al. (2003) reported dual FRET molecular beacon assays, where the donor probe was labeled with either Eu3+ or Tb3+ complex of DTPA-csl24-ethylenediamine (and no quenchers attached). For the Eu3+ complex, the acceptor probe was Cy5-labeled (and no quenchers attached) and for the Tb complex, the acceptor probe was labeled with Cy3 or ROX as a fluorophore and with dabcyl as a quencher. They demonstrated that these pairs of probes detected DNA targets ( 50-mer) with high S/N. 

Figure 17.9 Concept of photodynamic molecular beacons (a) the singlet oxygen formation via energy transfer from photosensitizer is prevented due to transfer of the energy to the nearby quencher (b) singlet oxygen formation after the spatial separation of the photosensitizer and quencher...

Finally, there have been reports that deal with other forms of spectral detection. A platinum (Il)-coproporphyrin reagent has been evaluated for phosphorescent labelling of oligonucleotides. The presence of the label had little effect on conjugation, and labelled primers were effective in PCR reactions. A silicon nanoparticle conjugated to ODNs acted as a luminescent label, and a molecular beacon (see later) has been prepared which contains a photoluminescent dye (Ru(II)(bpy)3) and the luminescent quencher Black Hole Quencher-2 . ... 

Molecular beacons (MB) are stem-loop hairpin oligonucleotide structures that have a fluorescent dye at one end and a fluorescence quencher at the other. In the hairpin state, the quencher and fluorophore are in close proximity and therefore there is no fluorescence from the probe. However, when the MB binds to a complementary oligonucleotide as a duplex then the fluorophore and quencher are separated and the fluorophore can emit fluorescence. They are particularly useful in monitoring reactions with time, e.g., in PCR, " rolling circle amplification, hybridisation, telomerase activity, ligation... 

The fluorescent ddA 5 -triphosphate derivative (163) was shown to be an effective substrate for terminal transferase, and various DNA polymerases. The resultant DNA could then be detected by fluorescence spectroscopy. A molecular beacon DNA probe incorporating a donor and a quencher dye has been reported, " which shows high sensitivity and dynamic range. Such molecular beacons are anticipated to have use in DNA/RNA and pro-tein/DNA/RNA interactions. 

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