Visual OMP^TM provides a variety of tools for designing primers and probes for working with targets containing a SNP. The PCR experiment can be designed either with two probes, one for the wild type and one for the mutant type, or it can be designed with two allele specific primers for the strand containing the SNP and another primer for the second strand. When designing probes, one has the option of designing a traditional probe pair for the SNP or designing an allele specific beacon probe pair. The allele specific design can also be accomplished with either an ARMS scorpion or an ASO scorpion.

When an allele specific probe pair is designed in Visual OMP^TM, the user is asked to specify the variation against which to design the probes. Visual OMP^TM will then consider all the possible probes that meet the user’s size criteria and check them to make sure there is no thermodynamically favorable hybridization with any other portion of the target or any other species in solution. Visual OMP^TM will present the user with a solution set of the best probe pairs for the allele. The user may then run a simulation to determine the expected concentrations of all the species expected to form in the PCR reaction.

The design of allele specific PCR primers by Visual OMP^TM designs a pair of primers to amplify the wild type and mutant type sense strand and a single primer to amplify the anti-sense strand. These three primers will be chosen based on parameters which can be set by the user. They will be designed to avoid unwanted thermodynamically favorable interactions with each other and with other unplanned sites on the target. Solution sets of the best candidate primers will be presented to the user which can then be evaluated in a simulation to determine the expected equilibrium concentrations of all species formed in solution during the experiment.