Different types of DNA extraction methods Different types

Different types of DNA extraction methods

• Different types of DNA extraction methods are available for different cell types. For example, the DNA extraction method for plant DNA is different from that of the blood. • In this article, we are going to discuss different types of DNA extraction methods which are mostly used in genomic labs. We will focus on the principle and the mechanism of each type of DNA extraction method.

• We will compare each DNA extraction method based on their performance and yield. Further, we will also discuss the advantages and limitation of different DNA extraction methods.

What is DNA extraction • “Extracting DNA from the cell” this is the simplest explanation for DNA extraction. • Several definitions of DNA extraction are enlisted here, • “Isolating DNA by disrupting cell wall/cell membrane and a nuclear membrane is called a DNA extraction”. • “Isolation of DNA by breaking the cell membrane and nuclear membrane with the help of chemicals, enzyme or physical disruptions is defined as a DNA extraction”. • Or simply, “isolating nucleic acid from rest of the cell organelle is called nucleic acid extraction or DNA extraction”.

How to obtain DNA • First, we will understand the anatomy of the cell, roughly. The cell is made up of cytoplasm and cell membrane/ cell wall. The cytoplasm contains several organelles such as mitochondria, ribosomes, nucleus, endoplasmic reticulum etc. • The animal cell does not have the cell wall, plant cell and (most) bacterial cells contain the cell wall.

• So if we want to isolate DNA we have to break cell wall/ cell membrane and nuclear envelope as well. Also, we have to remove other cell organelle debris. In the final step, we have to precipitate and purify the DNA.

• Lysis of cell wall/ cell membrane: • Chemical disruption • enzymatic disruption • Mechanical disruption • Lysis of nuclear membrane: • Chemical lysis • Enzymatic lysis • Removing cell debris • Centrifugation

• The nuclear membrane and cell membrane is made up of protein and lipids almost. Hence the same types of chemicals can work for both. • Chemicals such as SDS, CTAB, Tris and other detergents can lyse the cell wall/ cell membrane by solubilizing it. • Each chemical has a different function to play which we will discuss separately in each method.

• Enzymes such as proteinase K, peptidase, protease disrupt proteins by digesting it. • The enzyme works better than any other chemicals because it directly targets bonds between the amino acids and digests the protein. • Once the cell wall or cell membrane lysed, there are no compartments inside the cell hence all the cell organelles are mixed into the solution. By doing high-speed centrifugation DNA remains in the solution and the other cell debris settled into the bottom of the tube.

• Moreover, the DNA extraction method varies depending upon the type of cells. Take look at some example here, • The cell having a soft cell wall: some of the bacteria have a very smooth and soft cell wall. For example, M. tuberculosis has a smooth cell wall. By only heating the bacterial solution we can lyse cell wall. • The supernatant can directly be used for the PCR. Even, by putting the bacterial culture directly into the PCR tube for 15 minutes at initial denaturation we can directly get the good quality of result in PCR.

• However, the addition of a simple lysis buffer during heating will increase the yield and quality of DNA. • The cell having a harder cell wall: Plant cells have pectin and other polysaccharides present in their cell wall. This pectin protects the cell from mechanical damage. Therefore pectin provides additional strength to the cell wall of the plant. • Some of the fungus, algae and bacteria also have hard cell wall for surviving in harsh conditions. For extracting DNA from this type of cells, we have to modify protocol with a combination of mechanicalchemical- enzymatic method.

• Mechanical lysis is an important step in the isolation of DNA from pectin-rich cells. For doing this mortar pestle, grinding and liquid nitrogen is used. • Read more on plant DNA extraction method. • The cell having a cell membrane: The cell wall is not present in animal cells. A combination of the enzymatic and chemical method is most suitable for the DNA extraction from animal cells, however, each method individually performs the best. • The phenol-chloroform method is one of the best choices for animal cells.

How to do mechanical lysis • Take plant tissue and grind it with a mortar and pestle. Grind it well, and add liquid nitrogen carefully and again grind it even harder until the tissue becomes powder. Finally, add lysis buffer or DNA extraction buffer. Grind it till it becomes homogeneous. The tissue is ready for DNA extraction. • Additionally, we can add an enzyme to this homogenized solution and incubate it for an hour. The combination of mechanical- chemical and enzymatic lysis helps to extract good quality of DNA from the plant cell. This combination most probably gives the best result.

Physical lysis with the help of extraction buffer and liquid nitrogen.

Different types of DNA extraction methods

• DNA extraction methods are broadly categorized into two categories: 1. Chemical-based DNA extraction method. 2. Solid-phase DNA extraction method