I've been questioned about the thermodynamics of my siRNAs molecules. It is well described that the strand with less stability at 5' has a higher probability to be incorporated at RISC complex.

I've been using software like siDirect to design my siRNA molecules for years, they take account several algorithms (that include thermodynamics analysis) to predict best siRNA molecule to a specific target, but this software don't return the thermodynamics of the molecules.

Last week an referee requested to add thermodynamics information of my siRNA molecules in order to confirm which strand is actually been incorporated at RISC. I tried some software like SFold with no success as they only analyze one strand each time.

Does anyone have a good suggestion?

Thank you.