Molecular Beacon Design
Beacon Designer™ designs optimal molecular beacons for routine qPCR and NASBA® assays. The program automatically selects a stem of appropriate length (5, 6 or 7 bp long) for optimal beacon Tm. These beacons are not only have a suitable Tm, but are also free from runs, repeats and dimers for maximum signal fidelity. The program displays the graphical structure of the beacon along with its secondary structures.
Read the tech note on molecular beacons.
Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.
You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.