Electrophoresis: only seperate DNA by size!? - (Aug/10/2006 )
Hi all,
I have an idea regarding DNA charge and electrophoresis.
DNA is negatively charged because of its phosphate backbone which has a negative charge. So, the more DNA you have (more phosphates), the DNA would be more negatively charged and therefore is more attractive to the positive electrode. Thus, the DNA will move faster.
Does it make any sense?
Thank you for any comment! 
William
on the other hand, smaller the DNA is, faster it will go threw the "holes" of the gel
You are right, but as Missele says, the larger fragments will be more obstructed by the gel, and thus the smaller fragments move fastest.
But an effect of your observation is that increasing voltage has a PROPORTIONALLY larger effect on the larger bands, so that the difference in migration between the large and small bands will decrease. The smaller fragments still migrate faster though, and the ladder makes sure that your measurement of the size is still correct.
This phenomenon can be seen when you run Maxam-Gilbert sequencing lanes using 5'-end labelled DNA.
The G+A marker lane that I use as standard runs approximately 1.5 bp faster than the DNase I-cleaved material. This is because, although they are exactly the same length, the marker lanes fragments each contain one additional phosphate residue and hence migrate that little bit faster.
You have to remember this when pairing up bands otherwise you get the sequence wrong.
I have an idea regarding DNA charge and electrophoresis.
DNA is negatively charged because of its phosphate backbone which has a negative charge. So, the more DNA you have (more phosphates), the DNA would be more negatively charged and therefore is more attractive to the positive electrode. Thus, the DNA will move faster.
Does it make any sense?
Thank you for any comment!
William
I read a cool paper once that had video footage stills of DNA migrating through a gel (dammit, but I can't find it now!!!!!). The DNA migrates as a blob, until it hits an agarose fibre. Then it untangles and slides around the fibre, which is a slow process (especially as the DNA can go around both sides of the fibre - think of a piece of limp spaghetti over your finger). The longer the DNA fragment, the slower the process. After the whole fragment is past the agarose fibre, it reforms into a blob.
Imagine this happening hundreds or thousands of times. The short pieces of DNA will go through this cycle much faster than the longer ones, which might not even get back to the blob stage before hitting another agarose fibre. Remember also that the phosphate group is just a small part of a nucleotide; take the extra mass into account, and the increased attraction by charge is negated by the increased inertia, as much as the "sliding around the agarose fibre" effect.