Gel Electrophoresis

Introduction

Gel Electrophoresis is a unique process by which we use electrophoresis to differentiate DNA, RNA, and other protein-generated molecules. Electrophoresis is a process in which we use electricity and special gel or Matrix material to move the particles along with the circuit. In this method, we use gel with tiny pores applied with a high electric field. The entire concept of Gel Electrophoresis is that smaller DNA particles will travel at a greater distance than the larger DNA particles. 

As mentioned above, the entire field filled with the gel  is applied with an electric field. There are two ends in this gel field, one connects with the positive end of the battery, and the other connects with the opposing end. Gel Electrophoresis works based on DNA and RNA being acidic particles. The acidic content of these genetic materials is phosphoric acid. 

The treatment according to which the entire process works will likely be based on charged particles in the genetic material. If one wants to differentiate between the RNA and DNA, there’s a chance that Gel Electrophoresis gives the correct way to do so. The protein gets folded up due to the treatment. There is a possibility that the proteins take different shapes, sizes, and more in the process. Agarose Gel Electrophoresis is one of the most common ways out there. 

Gel Electrophoresis

As the name suggests, Gel Electrophoresis uses a special gel. This gel is something that we eat, and it is made up of different items such as polysaccharides. When we talk about polysaccharides gels, then one of the best in the most used electrophoresis is agarose. Agarose is very dry and comes in powdered flakes, but when manipulated precisely, you can get a suitable electrophoresis medium. You can also use the polyacrylamide gel.

Hydrogen bonds hold up the gel in this matrix, and these form many small poles responsible for attracting the genetic particles with the charge. There are unique hollow indentations called the wells at the end of the entire gel wall pocket. These wells are the places where DNA samples are placed.

The end of the gels is known as wells on where the DNA is stored when these fragments are provided up with a high electric field with specially positioned positive electrodes. 

Movement of DNA Segments in Gel  Electrophoresis

DNA segments are most probably particular segments found by DNA electrophoresis. One of the wells is reversed, for a DNA ladder. The DNA ladder is a standard reference with a known length, and also it has a standard reference quantity nucleotide that could be compared with the unknown DNA. 

The following process in Gel Electrophoresis will be turning on the power. Once the power is supplied to the field, the DNA molecules can quickly start moving towards the cathode for the so-called positive terminal due to their negative charge. As we all know, the sugar-phosphate born provides an acidic medium to the DNA; it quickly gets attracted to the positive terminal. When the power is on, the gel is said to be running.

The movement of charged molecules is called migration. Molecules migrate towards the opposite charge. A molecule with an opposite charge will be pulled towards the positive end of the body. Smaller molecules migrate through the gel more quickly and therefore travel further than larger fragments that migrate more slowly and will travel a shorter distance. Hence the charges will get separated easily. 

Visualisation of DNA Fragments

Once the electrophoresis is complete, and the length of DNA is displayed on the agarose gel, one needs to look at the DNA fragments. The DNA is stained with the unique DNA binding dyes and it takes on colours. The special dyes  are responsible for the visualisation of the DNA very quickly.

Visualisation of DNA is dependent on particular types of lights. If the reaction of DNA fragments with the other dyes is not suitable, you cannot expect a bright colour to be visualised out there. UV lights are used to visualise these DNA fragments and could help locate the exact positions of these DNA fragments.

Electrophoresis will help you to differentiate between different DNA fragments of various lengths.

DNA is negative in charge; hence when a specific field of electric current is present to the gel, DNA will move towards the electrode, which is positively charged.

Agarose gel electrophoresis is one of the most used matrices in the entire process of DNA fragmentation. The concentration of agarose plays a crucial role. 

When the agarose concentration is relatively high, it denotes a dense matrix. Smaller fragments of DNA get separated very quickly, and hence you can get a variation in the result depending on the size of the DNA fragment.

Gel pores’ dimension or gel concentration, electrophoresed DNA size, Buffer ionic strength, the voltage used, and the intercalating dye concentration affect Gel Electrophoresis. 

Application of Gel Electrophoresis

There is a massive application of Gel Electrophoresis in the current scenario where DNA is being manipulated and used in various tests and research. One of the widely used applications of Gel Electrophoresis is none other than DNA fingerprinting. Fingerprints are something that is unique to every individual, and they can be detected according to one’s DNA. The forensics often get different DNA samples from the crime sites, which are further examined and compared with the suspected people to get accurate results.

The so-called “gel,” in this case, will denote the entire matrix, which is the one that contains the target molecules. In most cases, the gel is a crosslinked polymer whose composition and porosity are chosen based on the specific weight and composition of the target to be analysed. When separating small nucleic acids (DNA, RNA, or oligonucleotides) or proteins the gel usually comprises different acrylamide concentrations and a cross-linker that produces different sized mesh networks of polyacrylamide. 

Conclusion

Gel Electrophoresis is used to separate fragments of DNA under the influence of electricity. 

Gel electrophoresis is used in DNA fingerprinting and in the field of biotechnology.