When we prepared a PFGE Southern blot to estimate the physical/genetic distance in a genomic region, we used an initial pulse time of 1 second and final pulse time of 120 seconds with a linear ramp to separate the DNA digested with rare cutting restriction enzymes. Why was the pulse switch time of 1 – 120 seconds used?
The geometry of PFGE apparatus usually leads to using equal times in each direction eg 60:60 or 45:45 seconds so your timing is unusual. The change in voltage direction changes the conformation of the running DNA fragments as does the angle that they are run at so three ideas may be possible. A previous user has used FIGE and found that these times work and has simply tried to transfer them to PFGE. The user has found empirically that this set of conditions works and although the running angle will be very odd it may give separation in the size range required. Or possibly someone was trying to set up 60:60 for the run and has ended up adding both times to the same switch. The question is does this switch time work well for your experiment and separate well in the size range required
it is possible that the previous user knew that ramp times give good separation in one size range at the expense of other sizes ans thought that you get the best of all separation by ramping through all reasonable times to try to get good size separation in all ranges. It is best to get good separation in the sizes that you are interested in so you should choose a ramp to suit yourself and it will give good separation and also save time on the total run time
Aayudh- As Paul Rutland indicated the idea is to enhance separation of chromosomes (or segments) that are similar in size or difficult to resolve for another reason. When we've done PFGE we had to empirically "tweak" conditions quite a bit to separate similar-sized chromosomes, and that was likely the case for whoever published the protocol you used. With such a wide range they may have been trying to optimize resolution of fragments over a very wide range, which is difficult. Although ramping is common it is typically performed over a narrower range of times than that. I suggest you simply contact the authors of the study from which you took the conditions and ask why they chose those.
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