Effective molecular beacon probes can be designed with the aid of Visual OMPTM. Molecular beacons are structurally similar to the tradition single strand hybridization probe except that the ends of the beacon contain equal length self-complementary segments, which, in the free state, will bond to each other forming a loop terminated by a blunt end stem. The ends of the stem have a fluorophor attached to one side and a quencher attached to the other side, so that it is self quenching in the unbound state. When the beacon attaches to a target sequence, the fluorophor and quencher become separated in space allowing the sample to fluoresce.
Visual OMPTM will check for the thermodynamic contributions of base pairing and nearest neighbor effects and secondary structure to determine the best structure for both the probe and stem of a molecular beacon probe. The user will be presented with a list of the best candidate structures for molecular beacons and their thermodynamic parameters and allow these structures to be modeled for their interactions with all species in solution.