Restriction Enzymes

Now that we can copy lots of DNA, that means we can mess with our samples in the lab to analyze them. One of the most important things that scientists will do is chop up the DNA with restriction enzymes. These are natural enzymes made by bacteria (and other prokaryotes) that will break the two strands of DNA.

Remember, these are enzymes, so they do not just cut wherever they feel like it. Enzymes are very specific to their substrate. So these enzymes will bind only to specific sequences of DNA. Each restriction enzyme has its own unique substrate. As a result, cutting up DNA by putting it into a solution with restriction enzyme A will result in different pieces than one placed in a solution with restriction enzyme B.

Here is an example of the way in which one restriction enzyme may cut up DNA. It will locate the sequence shown, and then chop up the DNA along the blue line. It will then move on and try to find that same sequence again.

Often, the same sequence can appear many times along the same DNA strand. Remember, all individuals have unique DNA sequences, which determine their alleles. This means that chopping up my DNA with restriction enzyme A may result in 30 pieces, but chopping up someone else's DNA with the same restriction enzyme may result in only 5 pieces depending on how often that sequence occurs in our genomes.

Gel Electrophoresis

Once DNA has been chopped up in the lab, it can be placed into a gel. DNA samples (filled with all those fragments) are pipetted into the sample wells shown here. The gel has little pores, or holes, in it that DNA can make its way through.

DNA is actually negatively charged, so it is attracted to positive charges and repelled by other negative charges. In gel electrophoresis, a power supply is connected to the gel so that there is a positive side and a negative side.

Notice that the DNA begins near the negative side, so it will 'want' to make its way over to the far side.

In reality, these gels can look something like this image (often even blurrier than this depending on the sample and your lab equipment!). As a result, most diagrams you see for AP Biology will be simplified versions like those above and in the following section.

DNA Fingerprinting

More interestingly, however, this gel pattern actually will allow us to analyze individuals because everyone's DNA is unique, acting like a genetic fingerprint.

As long as the same restriction enzymes are used for each sample, unique DNA samples will lead to unique band patterns.

As a result, a DNA sample found at a crime scene, for instance, can be analyzed and compared to DNA samples from given suspects. The suspect whose gel bands match the sample would be the individual from whom the sample came.

In this particular image, you can see that Suspect 2's bands match the sample because their DNA fragments were the same lengths after being exposed to the restriction enzymes.

Paternity Testing 

This same methodology can be applied to paternity testing as well. Remember that these bands are made of DNA fragments, and DNA comes from one's parents. So half of your DNA came from your biological mother and the other half from your biological father.

So you should see bands in common with both parents. All of a child's bands should be accounted for by looking at both parents. Think of it this way: a child has 4 DNA bands. They had to get them from somewhere - their parents, of course. So we should find those bands in their parent samples.

If we compare the mother and child DNA in this example, we see that they share two DNA fragments (highlighted in red). However, the child's other two strands do not match the mother, and therefore must have come from the other parent, the father. In order to determine who is the father, we just need to compare the DNA bands of the different men to those bands that are unaccounted for.

We can see some bands in common with both men 2 and 3 (highlighted in blue). However, man 2 is the only one individual who could have supplied all the DNA from the child that did not come from the mother. Therefore, man 2 is the father.

Plasmids & Conjugation

In order to understand some of the most recent developments in genetics, we will have to review a little information about bacteria. Recall that bacteria have circular chromosomes (see the blue DNA here).

However, bacteria also can have plasmids, which are also circular DNA, but they can be expressed and replicated independently from the rest of the DNA.