If A and B sequences are partially complementary to C, what would be the total Tm value of the system? How can I determine it theoretically by using software?
But I thik that the best way is to empirically determine the optimal Ta by using a gradient thermal cycler such as the BioRad CFX or by running separate PCR assays over a temperature range.
If your consensus in silico Tm is 62C, u can try your PCRs between 54C and 60C.