Whats a Gel?

In Hollywood, people seem to believe that science is a bunch of men and women wearing lab coats and safety goggles all diligently mixing various colored liquids together. After many mixes and exasperated sighs, the main character suddenly has an idea and mixes yet another two chemicals together which then begin to glow a strange green color. The men in women then turn and smile at each other because clearly they have just discovered science.

For isolating pure science, we are proud to present you with this Nobel Prize.

Now, to be honest, that isn't really how it works. 

Except if you are running a Gel. 

A Gel is generally done directly after a PCR. Those of you who have read our previous blog posts will know that PCR is a process that copies one section of DNA thousands of times. For those of you who haven't read our previous posts CLICK HERE!

The problem with PCR is that, just like everything in life, it doesn't always work out the way we want it to. 

Personally, I blame Gremlins. 

If the PCR didn't work, we need to know. That's where the Gel comes in. 

To begin, we take a little bit of the stuff we got from the PCR and mix it with a fancy dye. Then we take this and put it in the edge of a jello-like block (thus the name Gel). 

We run an electrical current through the Gel which acts like a vacuum cleaner and sucks the DNA from one side of the gel to the other. 

Imagine now, if you will, a playground at an elementary school. A tiny 6 year old kid can get from one side of the playground to the other in almost no time. This is because they can easily slip through all the little nooks and crannies and tunnels and such. Now imagine a sumo wrestler trying to move through this playground. He would move much slower because he would have a lot of trouble getting through the same tiny areas that the 6 year old could go through.

He'll figure it out eventually.

 A gel works the same way. Smaller pieces of DNA will get sucked through the gel much faster than larger pieces of DNA, which will move faster than even larger pieces of DNA. And so on. This means the DNA is separated out by size. Now if you remember, the PCR produces identical copies of a piece of DNA, which means that all of these copies are the same length. Since it is the same size it moves the same speed, and since it moves the same speed it will move the same distance. The special dye that we mixed with the DNA glows under a blacklight. If the PCR didn't work at all, we won't see anything, but if it did, we will see something like this. 

Each stripe is a different PCR. Don't worry, they won't mix. 

Now, some of you might be wondering "Isn't PCR only supposed to make one piece of DNA? The bit on the left has lots of stripes, which means lots of different sizes, which means lots of different pieces of DNA." 

If you thought that then you are absolutely right! If the PCR worked right we will only get one band. If we get more than that, we probably had a contaminate somewhere. The bit on the left is not a contaminate however, that is what is known as a ladder (because it kinda looks like one). 

See the resemblance?

A ladder is a mix of a whole bunch of different sizes of DNA. We know how large the DNA in each stripe on the ladder is, but we don't know how large the DNA from our PCR is. By comparing the PCR stripe with the stripe it is closest to on the ladder, we can make a rough guess as to what size the PCR DNA is. It basically acts like a DNA ruler.

So in short, a Gel lets us see, if our PCR worked, if our DNA is contaminated, and it lets us make an approximation of the size of the DNA. 

That's all for now! If you have any questions, fell free to post them in the comments section.

By Ben Segee