Molecular beacons design

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... 

The design of hybridization formats that enable important changes (fluorescence intensity increase or wavelength shifts) in the presence of the targets is the focus of intense research because their use can simplify the analyses in vitro and provide the possibility of applications in living organisms. The most frequently used involve binary probes (35), competitive hybridization probes (18), linear probes with only one F (2, 5, 16, 29, 31), and molecular beacons (MBs) (39-41), (Fig. 3). 

DNA- binding aptamers have been designed to bind to mRNA, g-quad-ruplexes, Tenascin-C, a protein found in the tumor matrix, and to thrombin. Aptamers have been selected as inhibitors of HIV-1 integrase, human RNase Hl, human pro-urokinase " and for the design of molecular beacons. An allosteric aptamer has been designed for binding as a colorimetric probe for cocaine. ... 

The loop sequence of the tpy-modified DNA strand was designed such that the strand could hybridize to a molecular beacon [Fig. 16(a)] only when in its extended, linear form [Fig. 16(h)]. Upon hybridization to the tpy-modified DNA, the molecular beacon switches from its closed, nonfluorescent form to its open, fluorescent form [Fig. 16(h)]. Both Fe and Zn form very stable [M(qjy)2] complexes and consequently, the circular structure adopted by the tpy-modified DNA strands in the presence of 1 equiv of these metal ions represented a steric barrier for its hybridization to the molecular beacon. The metal ion acted as an allosteric off switch for DNA hybridization (148). This study demonstrated that the incorporation of metal-binding ligands in nucleic acid strands can be used to create metal-dependent allosteric switches for the Watson-Crick interactions between the nucleic acid strands, a mechanism that may find applications in creating artificial systems with regulatory function. In contrast, in the presence of Cu + the DNA hybridization to the molecular beacon was energetically more favorable than the formation of circular stmctures from the tpy-containing DNA strands. Therefore, hybridization of a complementary ssDNA to the... 

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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