for the PCR primer what is better the hairpin or the self annealing? - (Nov/26/2006 )
i can;t much play with the sequence for the primers, so here are two options: either hairpin or self annealing (7 bases) as predicted by some tool on the web. according to your experience which one is less dangerous or less likely to happen. 
I would say the hairpin is less likely to happen because the same primer has to contort around on itself to make the hairpin, whereas it is much easier for a second primer to anneal to the first. In either case I wouldn't be too concerned over a 7 bp hairpin or dimer. Keep your annealing temperature high to prevent the secondary structure forming and ensure a good number of complementary bases in your primers and the PCR should work well. A touchdown PCR is a good PCR to perform under any conditions but is particularly helpful if you wish to avoid secondary structure.
well, i would hairpin as well, as the supposed conformation is hard to obtain by a primer.
how much is the self annealing length?
how much is the self annealing length?
any one choice of both may be better, depending on the 3 terminal.
if 3 terminal is protruding in hairpin or self annealing, it will not affect the application of primer.
Also look at the energy needed to open these structures, the less stable one is, the better it is, the more i would choose it.
the smaller of two evils. aka the structure which takes the least energy to break.
A 7bp self annealing is bad...
So would a large 3' hair pin.
Where is said hairpin and how large is it?
However if push comes to shove... 7bp self annealing is not fatal. As long as the binding segment of the primer has a decent melthing temperature ( ~58 Celsius - high enough tm) you should be okay.
thanx a lot guys! Self-annealing structure is 10 bps at the 3' end and hairpin is 4 bp ar 3' end.
i dont know about the energy, it is not written here. 
Tm is 60C.
well definitely hairpin as slight amounts of DMSO will reduce the issues of hairpon to form.
i am in agreement with Fred_33. The hairpin it is the smaller of two evils. 10bp of self annealing is very large.
thanx a lot! have a great day all! 