Are the primers mainly reducing primer-dimer or they are also protected from exonuclease activity of proof-reading polymerase? In other words, is the 3’OH of the primer exposed or available to low temperature before they are heat inactivated.

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The CleanAmp™ primers were created to reduce primer dimer and mis-priming however the CleanAmp group for the primers is situated on the internucleotide phosphate linkages.

This makes them very similar to a phosphorothioate or methyl phosphonate oligo which allows for nuclease resistance. I would recommend the precision primers since there are two CleanAmp groups for added nuclease stability. The CleanAmp primers 3’ OH group is exposed (not protected). The protecting group for the primers is different than for the CleanAmp dNTPs which is is blocking the 3’ OH.