Study of GEL ELECTROPHORESIS by a Research

Survived baby Guppies: 

Anyway when my surviving baby Guppies grew up they would have all kinds of cool traits:

These traits were carried by their DNA , their genetic material, which is found in their body cells. But sometimes I would forget which mother was the mother of the baby guppy, because there were several mother fish in the tank, and I wanted to keep track of inheritance in my guppy notebook. 

Biotechnology as emerging science : 

So what would have been very cool to have at that time? Some biotechnology! 

Biotechnology is the merge of biology and tech, and it's constantly changing! It includes topics such as PCR, cloning, and genetic engineering.

We're gonna talk about one of the bio technologies that could have, well potentially, helped me determine the genetic relationships of my guppies. And that biotechnology is gel electrophoresis! 

How Gel Electrophoresis Can Catagorize Molecules explained with the help of example 

Gel electrophoresis can be used to separate molecules based on how big they are (their size) and it's especially useful with  DNA. Let's look at DNA real quick. 

Study of DNA in Guppies cell: 

So here is a guppy cell. Here's the nucleus in the guppy cell. Here's the DNA in the nucleus of the guppy cell, and if you were to zoom into the DNA, here is a nucleotide which is a building block of DNA. 

See those phosphates in the nucleotides? They're a bit negative. Well they contribute a negative charge anyway to the DNA. So if we look at this whole DNA here it gives that DNA a negative charge.

That's a big deal, because gel electrophoresis which again separates molecules based on size relies on the fact that DNA molecules have a negative charge. 

GEL ELECTROPHORESIS

Okay, here's a gel electrophoresis machine. The point of the machine is to be able to have an electrical charge running through a gel so here's the gel typically made of agarose. 

Agarose Gel: 

Agarose is a polysaccharide polymer, and polysaccharides are carbohydrates. Yeah, usually agarose comes from seaweed. The agarose gel itself allows the DNA molecules to travel within it. 

Presence of Wells: 

One end of the gel has these holes called wells. The wells are where the DNA is placed into the place of the gel where the wells are a negatively charged, and the area of the gel here is positively charged. 

Where the DNA will travel towards?: 

So guess where the DNA will travel towards? Well since it's negatively charged, it's going to travel to the positive side. So typically when you're analyzing DNA in electrophoresis: 

Restriction Enzyme Role 

You use these restriction enzymes to cut the DNA up into tiny pieces. Restriction enzymes have the potential to lacerate up DNA in very specific areas, often related to the certain DNA bases, making restriction enzymes very applicable in biotechnology. 

So if I had baby guppy DNA and adult mother guppy DNA, and I want to compare them, then I would want to use the same types of restriction enzymes in both DNA samples. 

If same enzyme is used: 

If I used the same type of restriction enzyme, it should be cutting the DNA at the same identification points in the DNA samples. However, unless the mother and baby guppy are clones , those pieces that result after the restriction enzyme is done with them may be differently sized because the DNA of the baby and mother guppy had some differences in the sequence of their DNA bases. 

After cutting run into Machine: 

So the DNA samples both are cut into multiple pieces by the same type of restriction enzyme and then those samples are loaded into the gel sample1 and sample2. 

If we turn on the machine and let the DNA run through the gel, the DNA moves towards the positive side. But some pieces of that cut up DNA will move faster or slower than other pieces. 

Examples

Example 1: Mother and Baby Guppy Electrophoresis 

Longer DNA pieces tend to have a higher molecular weight and they take more time to make it across the gel when you juxtapose it to smaller DNA pieces which move at a faster rate.

So what you end up with is that these DNA fragments spread out with the longer pieces closer to the wells and the shorter pieces closer to this opposite side of the gel. 

Longer DNA Fragments vs. Smaller DNA Fragments 

These are called DNA bands, but to see them, you usually need to stain the gel itself and view it under a UV light. Now let's compare the DNA bands in this hypothetical simplified guppy situation. 

Bands are not similar: 

The bands aren't going to be identical, because these fish are not clones, but I can compare how similar the bands are and compare that to other mother guppy samples to look for relationships. 

Example: 

Let's say that we have three mother guppy samples to view and these are the only possible mothers from the fish tank. 

Which one appears to be the most related to the offspring in this case and has a high likelihood of being the mother? 

Example 2: Problem Solving with Gel Electrophoresis 

But we can't be 100% sure with this, It would be helpful for me to know the father guppy sample too because this will give you more insight. 

But if these are the only fish in the tank, it's a very high likelihood with this case. Also, you can use something called a DNA ladder! It's basically a sample that has known fragment sizes so if you run it in the electrophoresis machine, you already know the fragment lengths. 

DNA Ladder: 

Let's say this DNA ladder only had three bands, which is not usually the case. Since it's a DNA ladder, the base pair lengths are familiar. They are 500 base pairs, 2,000 base pairs, and 3,500 base pairs. Think for a minute...where would they fit in? 

Used as Reference: 

You can use this now as a reference to give estimates of how large the other fragments are when they're run alongside it.  

DNA Fingerprinting: 

It's also used as part of DNA fingerprinting. DNA fingerprinting is a way that one can recognize someone's DNA which can be very beneficial if you're trying to solve a mystery involving a crime scene. 

If you have a DNA sample from a crime scene, you can go through the steps of gel electrophoresis to compare it to the suspect DNA to see the likelihood of a match. In fact, you can take the results from gel electrophoresis and isolate genes of interest by something called southern blotting.