Question

In order to separate two DNA fragments of a similar size, what kind of agarose gel would you use and would you run it for a short time or a long time?

Answer 1

To separate two DNA fragments of a similar size, the ideal way is to run for a long time on a low-density agarose gel. Agarose gels that have less amount of agarose tend to facilitate the separation of molecules of similar sizes better than agarose gels with higher agarose content. This is because higher percentage gels retard almost all samples very much, and therefore both DNA molecules would be equally retarded. However, Agarose gels with a lower agarose percentage allow easier migration of DNA, which in turn allows for better separation.

Similarly, using longer separation times at a lower voltage difference would also promote separation of DNA molecules of similar size.