A TaqMan® probe graphical view is also available. The Tm calculation for TaqMan® probes is based upon the SantaLuia values Tm calculations utilize “nearest neighbor” thermodynamic values.
Beacon Designer also allows for the design of multiplex assays. Just like Molecular Beacon, TaqMan® probes are free of repeats and do not dimerize.
#BEACON DESIGNER RENEGADE SOFTWARE#
The software can also design and optimize primers and probes for TaqMan® assays. The software also gives us a graphical view of the Beacons probe.
The Tm calculation is highly accurate it is calculated by connecting to the mfold server. For example, for Molecular Beacons probes, Beacon Designer has an automatic Tm adjustment in which it automatically selects the optimal length such that the probe does not dimerize or form hairpin structures. The software is fully loaded with a number of features which make it the best option for primer and probe design. This software allows us to design Molecular Beacons probes for standard qPCR and for Nucleic Acid Sequence Based Amplification (NASBA), TaqMan® probes for standard qPCR and as well as locked nucleic acid (LNA)- substituted TaqMan® probes, other FRET (fluorescent resonance energy transfer) probes, and SYBR® Green primers for real-time detection of PCR products. For me, Beacon Designer is the best way to design qPCR primers and probes. Designing primers and probes for quantitative (also known as real-time) PCR (qPCR) is not an easy task because both the primer and probe sequences need to be considered during design.
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