How DNA moves through a electrophoretic gel

Well, I’m sitting at a conference at the moment, and have decided that it has been too long since I have indulged in the joy of biological teaching. Seriously! Stop laughing. Here’s the question I randomly chose for today:

The rate at which a DNA fragment moves in an electrophoretic gel is primarily a function of the fragment’s….

Isn’t it lucky that I totally by accident chose a question that can be answered pretty quickly? I know! Lucky! Anyhow, let me tell you a little about electrophoresis. This process is a step used in laboratories to study DNA, and is often taught in every single lab class in college simply because it’s rather simple and rather impressive. (Seriously–try this the next time you’re having dinner with your family “So I was studying deoxyribonucleic acid the other day, and needed to separate the fragments after I broke the bonds at known gene sites, so I simply ran an electrophoretic gel.” This is good for at least an extra helping of dessert and hours of proud bragging by your mom at the next knitting circle).

Well, how exactly does this work? DNA, as you might imagine, is huge. Think about the amazinhg amount of information stored in the genetic code–all that information just sitting there waiting to be expressed. When we study DNA, we usually want to study a particular section, or a particular gene. We do this by cutting the big string of DNA into fragments using enzymes. We then copy the DNA (lots and lots and lots through PCR which I’ll explain in a later post) and then somehow have to pick out the genes we want to focus upon.

This is where electrophoresis comes in. An electrophoretic gel is basically really stiff Jell-O. The gel is melted and poured into a rectangular mold, and 8 (or so) wells are formed in one end of the solidified gel. These wells give us a place to put the DNA. Now, DNA has a charge. Due to it’s chemical make up and all that jazz, it has a an overall negative charge. At this point, we want to separate the DNA into its different fragments, so some smarty somewhere decided to use that overall negative charge to do just this. The gel (with its wells filled to the brim with DNA in a liquid medium) is subjected to an electrical current. The DNA fragments are pulled through the pores of the gel as it is attracted to the positively charged energy at the far end of the gel.

Now, the DNA separates depending upon its size. The bigger the DNA fragment, the harder it is to force it through those tiny, tiny pores in the solid gel. Therefore, the bigger (or longer) the DNA fragment, the more slowly it moves through the gel. After a predetermined amount of time, the electrical current is removed, and the gel is stained with some horrible substance that causes DNA to glow under a black light. You then take a picture of the gel and look at the bands (see the picture above) and the ones that are furthest away from the wells are the shortest, while the ones closest to the wells are the longest.

So, back to the question:

The rate at which a DNA fragment moves in an electrophoretic gel is primarily a function of the fragment’s:
A) Length
B) double helical structure
C) Radioactivity
D) Degree of methylation
E) Adenine content

Can you pick out the correct answer now? Movement through an electrophoretic gel is strictly due to size, therefore the answer is “A.”

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