Oligonucleotides molecular beacons

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... 

Molecular beacons (MBs) are hairpin-shaped oligonucleotides that report the presence of specific nucleic acids. The MBs have been immobihzed by Tan and co-workers [27] onto ultrasmall optical fibre probes through avidin-biotin binding. The MB-DNA biosensor detected its target DNA molecules, in real time, with selectivity for a single base-pair mismatch. This MB-DNA-biosensor was used by Perlette and Tan [28] for real-time monitoring of mRNA-DNA hybridization inside a living cell. 

Thomas A, Smith HR, Willshaw GA, Rowe B (1991) Non-radioactively labelled polynucleotide and oligonucleotide DNA probes, for selectively detecting Escherichia coli strains producing Vero cytotoxins VTl, VT2 and VT2 variant. Mol Cell Probes 5 129-135 Thompson JS, Hodge DS, Borczyk AA (1990) Rapid biochemical test to identify verocytotoxin-positive strains of Escherichia coli serotype 0157. J Chn Microbiol 28 2165-2168 Tyagi S, Kramer FR (1996) Molecular beacons Probes that fluoresce upon hybridization. Nat Biotechnol 14 303-308... 

Figure 2.8a. Schematic representation of excimer-monomer switching molecular beacons (EMS MBs). EMS-MBs were dually labeled with pyrene at both 3 and S ends of single-stranded oligonucleotides with a stem-and-loop structure. In tlie absence of target DNAs. the slem-close-shaped EMS MBs predominantly emit the exclmer fluorescence (yellow-green). Upon hybridization with target DNAs, the EMS-MBs undergo the ilynamic conformational change to emit the monoincr fluorescence (pale Uue).

Vet JAM, Marras S A E (2004). Design and optimization of molecular beacon realtime polymerase chain reaction assays. Oligonucleotide Syn. Meth. Appl. 288 273-290. 

Molecular beacons are oligonucleotide probes designed originally for the detection of nucleic acid sequences (Tyagi and Kramer, 1996). They generally have a hairpin shape, which brings into close contact fluorescence reporters bound... 

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