Question

What is the primary reason that DNA gel electrophoresis is usually undertaken using an agarose gel and not an acrylamide based gel as in protein electrophoresis?

Answer 1

It depends on what you are sequencing: if you are talking LARGE fragments, then an Agarose gel is the best option. You can adjust the size of the pores in the gel matrix by adjusting the amount of agarose: higher Agar content if you have small fragments, lower if you are talking Big Size...

If you are doing Sequencing (e.g. Chainstopper method as devised by Sanger) then Acrylamide gels are the obvious choice, as you will be dealing with small fragments: after all, you need to distinguish fragments that only differ in length with one base!

Answer 2

Gel electrophoresis is a technique used to separate DNA fragments according to their size.

DNA fragments are negatively charged, so they move towards the positive electrode.

Because all DNA fragments have the same amount of charge per mass, small fragments move through the gel faster than large ones.