PCR primers: hairpin and dimers? - what can I do to avoid this? (Dec/15/2005 )
I have designed primers for PCR but after checking I understood that they can both form hairpin structures and self dimers.....i cant change the primer sequence so I will order the primers but can I do anything to avoid hairpin formation or dimer formation later on in my PCR. thanx a lot!
If faulty primer design is unavoidable, hot-starting PCR (manual or use hot-start enzymes), using PCR additives such as DMSO may help.
please i want to know if i have this problem than my PCR is going to fail or maybe not.....sorry new to this feild....
as suggested above if u cannot change the sequence of the primer (which would be the easiest thing to do) it would be necessary to use a hot start Taq and keep the annealing temp fairly high - you could also try using touch down PCR where u start froma high annealing temp and decrease by 0.5oC per cycle for a number of cycles and hoep that u may get a small amount of product forming.
its always hard to predict if your PCR is going to work or not, having sub-optimal primers does not help.
Along with other suggestions from the rest - you could also try using really small amounts of your primer during the PCR... but i agree re-designing the primers would be easiest, adn might even be cheaper at the end of it all!