Does increasing or decreasing the density of agarose gel in electrophoresis separate similar sized fragments?

1 Answer
Mar 10, 2016

Adjusting the percentage of agarose will not help separate similar sized fragments.


A low density of agarose is used to separate large fragments, whereas a high density is used to separate smaller fragments.

However, when two fragments are of similar size, adjusting the percentage of agarose will not help much to improve the separation. In this case you will need to adjust the voltage and/or the run time.
Decreasing the voltage and/or increasing the run time (e.g. length of the gel) improves separation of similar sized fragments.

To further improve separation you can make small adjustments in the amount of material loaded and the composition of the buffer.