Taqman probes are used with Taq polymerase in the 5’ to 3’ amplification of DNA. The Taq probe contains both a fluorophor and a quencher in close proximity to one another which inhibits fluorescence in the probe hybridized to the target sequence or in excess probes in solution. When the target strand is amplified in the Taqman PCR reaction, the Taq polymerase, which is an exonuclease, will degrade the probe resulting in the separation of the fluorophor and the quencher. Thus the fluorescence of the sample will be proportional to the number of amplicons that have been created.
Visual OMPTM will allow the user to design efficient Taqman probes using thermodynamic parameters for base pairing and nearest neighbor interactions. The program will check the probe design for hybridization with undesired binding sites. Visual OMPTM also allows the user to include the thermodynamic effects of the fluorophor and quencher in the computations. The program has an extensive library of modifier thermodynamic parameters and allows the user to add their own data to the library.