Yesterday I suspected about the reaction buffer being the problem but now I have no doubts about it.
Here is a picture of my last PCR:
1-7: Taq platinum buffer + 0,5mM MgCl2 (final concentration)+ 0,8 mM dNTPs (final concentration) = A
8-12: SeqPrep buffer (MgCl2 and dNTPS incorporated in the kit)= B
1 and 13: A + polymerase
2: A + 30 ng DNA + polymerase
3: A + primers (about 1 uM final concentration)+ polymerase
4: A + 30 ng DNA + primers + polymerase
5: A + 30 ng DNA + primers + DMSO (7% final)+ polymerase
6: A + 30 ng DNA + primers + Enhancer (from the SeqPrep kit 1x final concentration)+ polymerase
7: A + 30 ng DNA + Primers + DMSO + Enhancer + polymerase
8: B + 30 ng DNA + Primers + polymerase
9: B + 30 ng DNA + Primers + DMSO + polymerase
10: B + 30 ng DNA + Primers + Enhancer + polymerase
11: B + 30 ng DNA + Primers + DMSO + Enhancer + polymerase
12: B + 30 ng DNA + Primers + dNTPs + polymerase
14: B + polymerase
15: newest Seqprep Buffer + polymerase
By simple observation of the PCR tubes after the PCR reaction I could easily note the precipitation on tubes 9,10 and 11.
The point is that the precipitation only appears when I combine the seqprep buffer with DNA or primers. Could it be posible that for some reason something is co-purifying along my DNA sample and only interfers with Seqprep buffer (and not with Taq Buffer) causing the precipitation? Or could it be posible that some contamination had happened in the Seqprep buffer (perhaps a funghi?) that only in the presence of DNA produces the precipitation? Remember that we use the same room for all the process and we do not use laminar flow cabinet.
I'm not sure if with Taq Platinum Buffer this is going to work (the amplification of my 12 kpb bands!) but al least I have no precipitation!