I have been trying to design primers and one of the primer criterion given is that any possible hairpins have a negative delta G value. I am confused about this as I would assume that a more positive delta G value would prevent the formation of these hairpins, which is undesirable in primers.
Some clarification on this subject would be great.
Paul Rutland
As you say the deltaG is a guide to both homo dimerisation or hetero dimerisation and in practice primers with deltaG lower than -9kcal/mole risk dimerisation and hot start enzymes or dmso addition or high annealing temperatures may be needed for clean amplification. Ideally delta G shoild be greater than -9 although this does not guarantee that the primers will be trouble free
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