How much hairpin loop effect in a PCR amplification?

PSarfati psarfati at
Mon Feb 15 10:50:09 EST 1999

>>I am working with some primers for PCR amplification. Can anyone suggest me
>>what level of hairpin structure I can afford in my primers? Does anyone have
>>experience of handling primers with large hairpin loops?

I suggest you search the wed (pubmed) for new strategy using molecular beacon.
In fact, hairpins are real problem depending on the stringency or specificity
you need in your PCR. You better use smal oligo programs for getting rid of
theses structures if possible.

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