![]() ![]() ![]() In the absence of a complementary nucleic acid target (analyte), the fluorescence of the fluorophore is quenched by the closely located quencher dye. ![]() In its classical design, a molecular beacon (MB) probe is a stem-loop-folded oligodeoxyribonucleotide with fluorophore and quencher dyes conjugated to the opposite ends of the hairpin (Figure 1(a)). Introduction: An Elegant Unimolecular Biosensor Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Furthermore, the signal is generated in a reversible manner thus, if the analyte is removed, the signal is reduced to the background. Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. Although, it may take some time to get used to working with this tool, a help menu is included, so you can understand the functions of each dedicated parameter.Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. In conclusion, Beacon Designer is an application that can help you design primes and beacons efficiently. The program also bundles a print preview feature, and it is possible to zoom in or out of different pages.īeacon Designer is able to design optimal primers based on standard reaction conditions, and you can view and change the conditions, such as nucleic acid concentration, temperature for free energy calculation, and others. ![]() You can also sort primers by making the program display the sense and antisense primer, and product on the basis of rating, position, length, Tm, and others. The results can be exported to XLS file format. It is possible to select the items that should be included in the final results report for beacons and primers, such as quality, position, length, and others. The program allows users to generate different beacons and primers, and you can save the data as projects. It provides accurate hairpin Tm calculation, and is able to display a graphical view of the designed beacons. Moreover, Beacon Designer can create molecular beacons for detection of wild and mutant alleles, and design beacons and primers for multiplex reactions. It bundles an automatic adjustment feature that can help you select the stem of appropriate length for creating an optimal beacon. There are several designs available and you can opt for a beacon, FRET, HRMA, MethyLight TaqMan, Scorpions, SYBR or TaqMan. The user interface may seem a bit overwhelming at a first glance, but this is only because this tool packs so many useful options. This application comes packed with all the necessary features that you’d expect to find in any professional software solution that deals with such a task. Beacon Designer is an application that can help you design PCR primes, usually used by molecular biologists in their studies. ![]()
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