Common PCR products are easily analyzed using standard agarose gel elecrophoresis. Anything between 0.1kb and 12-15kb can be separated and seen clearly in TAE agarose or similar buffers.
Why do you want to use PF-GE for this? Have you got very long PCR products?
Thank you Dr. Andrea Galli, just I want to separate very closed sized PCR products, differing in size about 10 to 15 bp in a multiple PCR reaction, I hope you got my point, thanks
Pulsed field in your case is not so necessary as usin high resolution gels i.e. PAAG or high precetage agarose gels (but its resolution quite lower than PAAG).
OK, Dr. Nandagopal Murugan I will try Polyacrylamide Gel electrophoresis method I think you gave a , good suggestion Dr. Andrii Tarieiev your comments are also valiable but still my question is remaining what is the best method for separation very closed products size (even they are of longer sizes)
It very much depends on the size range of your products. Separating fragments that differ by 10nt is very easy if the fragment is 100-200 bp in length, but it is very difficult if your fragment is 1000 bp in length. If you are in the 100-200 length region then polyacrylamide gels will work fine, but so will 2% agarose gels. If you are trying to work with substantially longer fragments then you will likely need to use agarose but really optimize the agarose concentration and the length of the gel. The longer the gel and the longer you run it, the easier it is to discriminate between similarly sized DNA fragments.
PFGE only works for very large fragments (typicaly 50 000 bp and more) that can only move through the gel end-on. Separation is based on the time required for them to reorientate in the switching electrical field so they can start moving again in the new direction. As the other respondents say, acrylamide is the best gel for the job and if run optimally it can resolve down to 1 bp size differences. A high percentage agarose gel (2 - 3%) or one of the speciality agaroses may well be sufficient for your purposes.
Omar, with that range of sizes high-density Agarose gel (2-2.5%) should work fine. PAGE is of course an alternative, because it gives very high resolution, but PAGE gels are more difficult to handle, in my opinion, so I try to avoid using them if I can.