Hi,

When I design oligos/primers to use in PCR etc, I usually look at secondary structures and mis-priming etc by using either mfold Tm server (secondary structures within oligo) or mfold 2-state Hybridization server for the primer-bindning.

Do you guys know of a method that can do both at the same time? I want to know which structure that will be the most probable to occur (like hairpin or primer-template hybridization). I know I can look at the Tm and delta-G, but would also like to see the full structure of what’s most probable.

Is there such a tool or is it too much to take into consideration when calculating free energies and melting temperatures?

Thanks