# What causes the DNA fragments to stop moving in gel electrophoresis?

I'm currently studying VCE BioChemistry, and we're studying the separation of DNA strings of different lengths via gel electrophoresis.

(This involves having 'clumps' of DNA at one end of a gel medium and applying an electric current, pushing the DNA strands across the gel. Different sized strands move at different speeds through the gel)

At some point, the strands stop moving such that there is a distribution of strands across the gel. What causes the strands to stop?
Surely they'd continue until the end of the gel.

If suppose the electric current could be stopped, thus causing the strands to stop moving, but how would one know when to stop the current?

• The DNA does run off the end of the gel. I will suggest that this question be migrated to biology.se – bobthejoe May 25 '12 at 5:12
• As for when to stop, most loading dyes will contain dyes that will run as a certain molecular weight. Knowing this, you know when to stop your gel. See openwetware.org/wiki/Agarose_gel_loading_dye for more details. – bobthejoe May 25 '12 at 5:14
• @bobthejoe: Electrophoresis, while being widely used in biology, is still a physical-chemistry concept at its root. This question deals with that concept, and thus is fine here, IMO. Also, if you want to suggest migration, use the flag option, that way we are guaranteed to notice it :) – ManishEarth May 25 '12 at 12:17
• @bobthejoe: I agree with Manishearth. Electrophoresis is definitely a chemistry technique in addition to being a biology technique. I expect the answer to this question has a lot more to do with chemistry, particularly the structure of DNA, than biology. – Ben Norris May 25 '12 at 16:39
• Also today it is quite common to have the DNA stain already in the gel while the electrophoresis is running (instead of adding a staining solution at the end of the run). This allows to follow the DNA run in "real time". – user1441 Apr 3 '13 at 20:55

There are electrophoretic methods where the molecules stop automatically like Isoelectric Focusing, but in the common agarose gel electrophoresis of DNA you mention this is not the case.

The DNA is negatively charged, it will move along the electric field you set up until you stop applying any current. It will happily move out of your gel if you let it run for too long.

To see the progress of your gel some dyes are usually added to the sample like bromophenol blue or xylene cyanol. They don't interact with the DNA, they just provide you a reference on how far your gel has run. You still need to have a rough idea how your samples run compared to those dyes if you want to use the full length of your gel.

As I understand it, the DNA strands don't stop, they just migrate at different rates and you have to stop the process (i.e. remove the electric field) at some point when you have a good pattern.

• Oh! So the dyes are added to the DNA before the electrophoresis? – Anti Earth May 26 '12 at 1:40

DNA Molecules may stop to move in agarose gel due to high molecular weight , the molecular weight of DNA affect its mobility in gel , the smaller the molecular weight the higher the speed of migration and long distance . large molecules tend to migrate slowly and they move short distance.

• Welcome to Chemistry.SE! Take the tour to get familiar with this site. Mathematical expressions and equations can be formatted using $\LaTeX$ syntax. For more information in general have a look at the help center. At the moment this reads more like a comment than an actual answer - could you elaborate a little more. With a bit more rep, you will be able to post comments on any question/answer. – Martin - マーチン Apr 28 '16 at 7:19