While sharing a number of similarities, plasmid DNA extraction and genomic DNA extraction exhibit numerous differences. Genomic DNA extraction allows for DNA extraction in both prokaryotic and eukaryotic cells, whereas plasmid DNA extraction usually only applies to bacterial cells with plasmids present due to eukaryotic cells seldom containing plasmids. Furthermore, genomic DNA extraction isolates all DNA (including plasmids) from a sample, whereas plasmid DNA extraction only isolates the plasmids themselves.

The uses of genomic DNA extraction and plasmid DNA extraction differ as well. Genomic DNA is commonly utilized in sequencing or polymerase chain reaction (PCR), while plasmid DNA is more frequently used in cloning or gene therapy. Obtaining a pure form of DNA through genomic DNA extraction proves difficult as the yield typically consists of a mixture of DNA types, including impurities. By contrast, plasmid extraction typically yields highly pure plasmid DNA.

Genomic DNA extraction necessitates a robust lysis procedure compared to plasmid DNA extraction. The more potent lysis method removes the cell membrane and thick cell wall (in prokaryotic cells) to release the genomic DNA. As a result, stronger lysis methods such as SDS and proteinase K are generally used to lyse prokaryotic cells. Plasmid DNA extraction, on the other hand, necessitates a mild alkaline lysis to obtain plasmid DNA from bacteria.

Following centrifugation, genomic DNA is obtained in the pellet while plasmid DNA is found in the supernatant. Since genomic DNA is larger and more complex than plasmid DNA, it requires more force to pellet it during centrifugation. Plasmid DNA is less complex and smaller, making it easier to separate from other components and appear in the supernatant.

2. Clarify DNA Gel Electrophoresis with the Aid of a Diagram

DNA gel electrophoresis is a lab technique for separating DNA according to its molecular size, which necessitates the use of gel. Agarose and polyacrylamide are two types of gel that can be used in DNA gel electrophoresis. Agarose is derived from seaweed, and its large pore size makes it the most common gel used in electrophoresis for separating DNA fragments. Electrophoresis entails applying current via the whole agarose gel containing the DNA fragments.

The gel is placed in the gel box prior to adding the DNA fragments to the gel well, which is situated toward the negative electrode. A buffer solution is poured into the gel box to cover the gel.

To make the DNA fragments visible, they mix with Bromophenol blue, which is used as an indicator of DNA in agarose gel electrophoresis. Bromophenol blue functions well for DNA staining because it has a slightly negative charge and moves in the same direction as the DNA fragments. Once stained, the DNA is added to the well, with one of the wells reserved for the DNA ladder. The DNA ladder serves as a standard reference and includes DNA fragments of various lengths. The size of the DNA fragments on the sample is determined by comparing their position on the gel to the fragments on the ladder. Current flows through the gel, causing the DNA fragments to migrate toward the positive electrode because the DNA molecules are negatively charged due to the phosphate groups in their sugar-phosphate backbone.

Several factors, including molecular size, charge, and shape, affect the rate of migration of molecules during electrophoresis. However, in DNA gel electrophoresis, migration rate is dependent on molecular size. As all DNA molecules have the same amount of charge per mass, the smaller the DNA fragment, the faster it moves through the gel matrix.

Sources:

Lakna, B. (2019, August 8). Distinguishing Genomic DNA from Plasmid DNA Extraction. Pediaa.Com. https://pediaa.com/what-is-the-difference-between-genomic-dna-and-plasmid-dna-isolation/

Chauhan, T. (2020, July 23). Bromophenol Blue and Xylene Cyanol for DNA Gel Loading Dye. Genetic Education. https://geneticeducation.co.in/dna-gel-loading-dye-bromophenol-blue-and-xylene-cyanol/

In order to differentiate between genomic and plasmid DNA extraction processes, Lakna (2019) explains the key differences between the two methods in an article featured on Pediaa.Com. Meanwhile, Chauhan (2020) talks about the usage of bromophenol blue and xylene cyanol for DNA gel loading dye and its importance in genetic education on his website.

Both resources provide valuable information and insights into the field of molecular biology and genetics, offering deeper insights that are useful not only for students but professionals as well. Through these articles, readers can learn how to apply various techniques and procedures when conducting experiments in these fields, and better understand the basics of molecular genetics.