I am trying to understand the "self complementarity" term in PCR primer design. As I understand, it is desired to have the score less than 4 matches for the 3' end to avoid heterodimer structure. But I didn't understand the logic of the score for self complementarity. Based on the NCBI primer blast, when I design the primers, it gives two parameters: "Self complementarity" and "Self 3' complementarity". What is the desired range for the first one to be able to design specific PCR primers without dimerization and why?
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