Gel Electrophoresis - Online Tutor, Practice Problems & Exam Prep

Gel electrophoresis is a technique used to separate and visualize DNA fragments based on size. Negatively charged DNA migrates through a gel matrix towards the positively charged anode when an electrical current is applied. Larger fragments move slower and remain closer to the starting point, while smaller fragments travel further down the gel. This separation allows for comparison against a reference DNA sample, facilitating size estimation of unknown fragments. Understanding this process is crucial for applications in genetics, molecular biology, and biotechnology.

Gel Electrophoresis

In this video, we're going to begin our lesson on gel electrophoresis. Gel electrophoresis is a technique used to separate and visualize fragments of DNA using a 3-dimensional gel matrix. It's important to note that DNA itself is a negatively charged molecule. This negatively charged DNA will be separated using gel electrophoresis by its size using an electrical current and an ion buffer solution. Towards the top of this gel, the cathode represents the negatively charged end of the gel, where the DNA samples are first loaded. The DNA will migrate away from the cathode towards the anode, which is at the bottom of the gel. The anode represents the positively charged end of the gel where the DNA sample will migrate towards.

Gel electrophoresis separates the DNA based on its size. The larger fragments of DNA move slower through the gel, meaning they remain closer to their starting point at the top of the gel. In contrast, the smaller fragments of DNA move faster through the gel and reach the bottom more quickly. Below, we can get a better understanding of gel electrophoresis. Notice that the gel is organized into lanes, almost akin to lanes at a bowling alley, with six different lanes in this example. At the top of each lane, the wells represent the starting place of the DNA. Each lane typically has a different DNA sample.

In the beginning, there is a reference DNA sample with known characteristics, and other lanes host DNA samples from different individuals, like individuals A, B, and C. Notice again that at the top of the gel, the cathode represents the negatively charged end of the gel where the DNA samples are loaded. At the bottom of the gel, we have the anode which is the positively charged end. Opposite charges attract, and the negatively charged DNA will migrate towards the anode, achieving separation through this gel matrix.

As the DNA migrates from the top of the gel to the bottom, each lane displays DNA fragments of various sizes. The bands throughout the gel represent DNA fragments. For example, in the reference lane, the fragment at the top, the largest fragment, is 1,000 base pairs. The smaller fragments migrate faster through the gel and are found towards the bottom. This allows for a comparison of DNA fragment sizes between samples and the reference, providing an approximation of the sizes using the reference.

Additionally, we have a graph showing the relationship between the DNA fragment size and the distance the fragment travels through the gel. The x-axis represents the molecular size of the DNA in base pairs, while the y-axis represents the distance traveled in the gel. The larger the DNA, the less distance it travels through the gel, remaining towards the top, while the smaller fragments migrate a further distance in the gel. Below, we have an image of an actual gel electrophoresis being performed, allowing us to compare the sizes of the DNA samples to the reference. This concludes our introduction to gel electrophoresis and how it is used to separate and visualize DNA fragments based on size. We'll practice applying these concepts as we move forward in our course. I'll see you all in our next video.

Gel Electrophoresis Example 1

So, gel electrophoresis can be used for many different reasons. Here we have an example that shows how gel electrophoresis can be used. It says, using the gel shown on the right-hand side below, determine which rabbit species are most closely related. We have four potential answer options below. Looking at this gel, notice that there are three different lanes, 1, 2, and 3. Within each lane, we have different species of rabbit: rabbit A species here, rabbit B species here, and rabbit C species in the third and final lane.

In order to determine how closely related the species are, what we need to do is compare the band pattern in each of the lanes. When you do this, you will find that the band pattern of rabbit A is very similar to the band pattern of rabbit C, and they share more DNA bands that are in common than any other combination. You can see that this band here is also the same. Maybe not this one here, but this one and this one—these here are all the same. Thus, there is a lot of similarity, and really the only differences that stand out between rabbit A and rabbit C are the bands that are being circled in these positions. These are the only ones that do not match up with each other vertically on the gel.

Because they have such close similarity in this respect, that means that these are the two rabbit species that are most closely related. Our answer is going to be answer option B here, which states rabbit species number 1 and number 3 are the ones that are most closely related, and that's simply because their band patterns match each other the best. Option B here is, therefore, the correct answer for this example problem. We will be able to get some practice applying these concepts as we move forward in our course. So, I'll see you all in our next video.

At a crime scene a blood sample was found and investigated using gel electrophoresis. Based on the gel, the blood at the crime scene belongs to which of the suspects?

• A. Jenny
• B. Bob
• C. Mike
• D. Lisa
• E. The blood at the crime scene does not belong to any of these suspects.

The parents of a new baby believe that the hospital sent them home with someone else’s baby. The hospital 

takes DNA samples from both parents and the baby. The DNA is investigated using gel electrophoresis. Do the parents possess their biological child or did the hospital give them the wrong baby?

• A. The parents have the correct baby, their DNA matches.
• B. The parents have the wrong baby, their DNA does not match.
• C. There is no way to tell using this gel.

Gel electrophoresis separates fragments of DNA based on which characteristic?

• A. Sequence.
• B. Level of methylation.
• C. Size.
• D. All of the above.

Why do the fragments of DNA in gel electrophoresis move away from the negative cathode?

• A. DNA is negatively charged and attracted to the positive anode.
• B. DNA is positively charged and attracted to the positive anode.
• C. DNA is negatively charged and attracted to the positively charged agarose gel.
• D. DNA is positively charged and attracted to the negatively charged agarose gel.

Here’s what students ask on this topic:

What is gel electrophoresis and how does it work?

Gel electrophoresis is a technique used to separate and visualize DNA fragments based on their size. DNA, being negatively charged, is placed in a gel matrix and subjected to an electric current. The gel has a cathode (negative end) at the top and an anode (positive end) at the bottom. DNA samples are loaded into wells at the cathode end. When the electric current is applied, DNA fragments migrate towards the anode. Larger fragments move slower and remain near the top, while smaller fragments travel further down the gel. This separation allows for comparison against a reference DNA sample, facilitating size estimation of unknown fragments.

Why do smaller DNA fragments move faster in gel electrophoresis?

In gel electrophoresis, smaller DNA fragments move faster because they encounter less resistance as they migrate through the gel matrix. The gel acts like a sieve, where smaller fragments can navigate through the pores more easily than larger fragments. As a result, smaller DNA fragments travel further down the gel towards the anode, while larger fragments move slower and remain closer to the cathode. This differential movement based on size allows for the separation and visualization of DNA fragments.

What is the purpose of the reference DNA sample in gel electrophoresis?

The reference DNA sample in gel electrophoresis serves as a size marker or ladder. It contains DNA fragments of known sizes, which are used to estimate the sizes of unknown DNA fragments in other lanes. By comparing the migration distances of the unknown fragments to those of the reference fragments, researchers can determine the approximate sizes of the unknown DNA fragments. This comparison is crucial for applications in genetics, molecular biology, and biotechnology, where accurate size estimation is necessary.

How is the gel matrix prepared for gel electrophoresis?

The gel matrix for gel electrophoresis is typically prepared using agarose or polyacrylamide, depending on the size range of the DNA fragments being analyzed. Agarose gels are commonly used for larger DNA fragments, while polyacrylamide gels are used for smaller fragments. The gel is prepared by dissolving the agarose or polyacrylamide in a buffer solution, heating it to dissolve completely, and then pouring it into a mold to solidify. Once solidified, wells are created at the top of the gel for loading DNA samples. The gel is then placed in an electrophoresis chamber filled with an ion buffer solution to conduct the electric current.

What are the applications of gel electrophoresis in molecular biology?

Gel electrophoresis has numerous applications in molecular biology, including DNA fingerprinting, genetic mapping, and the analysis of PCR products. It is used to verify the presence and size of DNA fragments, identify genetic mutations, and compare genetic material from different sources. In forensic science, it helps in identifying individuals based on their DNA profiles. In research, it aids in cloning, sequencing, and studying gene expression. Overall, gel electrophoresis is a fundamental tool for analyzing and manipulating DNA in various biological and biotechnological fields.