I'm attempting to automate primer design (specifically, primers for RPA, which requires longer primers [~30-35 nc] than PCR), and need to figure out how to calculate the free energy of a primer pair to check whether they form a dimer (or hairpin). How would I find the free energy when not all matching bases are consecutive? I'm trying to use the nearest neighbor method but am open to other methods if NN is infeasible.

  • $\begingroup$ There are many tools available for this. Why do you want to make a new one? $\endgroup$ – WYSIWYG Jan 18 at 17:19

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