All articles, DNA Extraction, ExploreDifferent types of DNA extraction methods

Different types of DNA extraction methods

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.

Outline if this article:

  • History of DNA extraction
  • Definition of DNA extraction
  • How to obtain DNA
  • Different methods of DNA extraction
  1. Enzymatic DNA extraction method
  2. Phenol-chloroform method for DNA extraction
  3. Silica- Column based DNA extraction method
  4. Magnetic bead method of DNA extraction
  5. Other DNA extraction methods
  6. Importance of DNA extraction
  • Advantages and disadvantages of DNA extraction methods

History of DNA extraction

The first DNA extraction attempt had performed by Friedrich Miescher in 1869. He had isolated the cell material and named it as the nuclei later on his student named it as nucleic acid. Although he accidentally developed a method for isolation of nucleic acid, he was not sure that what he isolated was DNA or not.

Later on, in 1958 Meselson and Stahl developed a full-function protocol for DNA extraction. The density gradient centrifugation protocol was the first protocol described by isolating DNA from E.coli bacteria.

The protocol of proteinase K enzyme method of DNA extraction was developed by Lahiri and Nurenberger in 1991. They also modified the protocol by using the Nonidet P40 and SDS.  However, the use of proteinase K in DNA extraction was reported earlier by Miller et al., in 1988.

The phenol chloroform isoamyl alcohol method which is most popular in recent days is developed by Joseph Sambrook and David W. Russell.

What is DNA extraction

Several definitions of DNA extraction are enlisted here,

“Isolating DNA by disrupting cell wall/cell membrane and nuclear membrane is called as 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 as nucleic acid extraction or DNA extraction”.

How to obtain DNA

Well, I don’t have the exact label to define this section, but still, I want to discuss this portion with you because it is important to understand how DNA is obtained from the cell.

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 bacterial cells contain the cell wall. I am not going to discuss each and every component of the cell wall or cell membrane because that is not the point of discussion.

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The image represents the general outline of how DNA can be extracted from the cell.

Ok, coming to the point,

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. Finally, we will purify the DNA.

This is the outline, we have to follow this steps for obtaining a good quality of 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
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The general flowchart of the DNA extraction procedure.

The nuclear membrane and cell membrane is made up of protein and lipids almost. Hence same types of chemicals can work for both.

Chemicals such as SDS, CTEB, Tris and other detergents can lyse 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 in 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. Because DNA is a macromolecule, by doing high-speed centrifugation DNA remains in the solution and the other cell debris settled into the bottom of the tube.

Further, 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, tuberculosis has a smooth cell wall. By only heating the bacterial solution we can lyse cell wall.

Centrifuge the solution and the supernatant can directly be used for the PCR. Even, by putting the bacterial culture directly into the PCR tube and place it 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.

Our series of articles on PCR,

The cell having a harder cell wall: Plant cell have pectin 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 mechanical- chemical- enzymatic method.

Mechanical lysis is an important step in isolation of DNA from pectin-rich cells. For doing this mortal pestle, grinding and liquid nitrogen can be used.

The cell having a cell membrane: The cell wall is not present in animal cells. A combination of the enzymatic and chemical method is mostly adapted for the extraction of DNA from animal cells, However, each method individually performs the best.

The phenol-chloroform method is most suitable for this type of extraction. 


How to do mechanical lysis

Take plant tissue in a mortar and pestle. Grind it well, now add liquid nitrogen carefully and again grind it even harder until the tissue becomes powder. Finally, add lysis buffer or DNA extraction buffer and grind till it becomes homogenized. The tissue is ready for the 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.

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

Different types of DNA extraction methods

Phenol-chloroform method of DNA extraction:

This method is one of the best methods of DNA extraction. The yield and quality of DNA obtained by the PCI method is very good if we perform it well. The method is also called as a phenol-chloroform and isoamyl alcohol, PCI method of DNA extraction.

The major chemicals of PCI DNA extraction methods are lysis buffer, Phenol and chloroform.

The lysis buffer contains Tris, EDTA, MgCl2, NaCl, SDS, and other salts. Here the components of lysis buffer help in lysis of cell membrane as well as nuclear envelope. The protein portion of the cell denatured with the help of chloroform, phenol and isoamyl alcohol which are organic in nature.

Role of chemicals:

Tris: DNA is pH sensitive, Tris buffer maintains the pH of the solution. Also, it interacts with the lipopolysaccharides of the cell membrane and makes them permeable, this will help in lysis of cell membrane.

EDTA: EDTA is a chelating agent and can be used to block DNase. DNase is an enzyme which lyses the DNA. However, every enzyme required cofactor to work properly. 

The chelator EDTA blocks the activity of DNase by blocking the cofactor binding site. It will work best in combination with Tris.

SDS: Sodium dodecyl sulphate is an anionic detergent which helps cell membrane and nuclear envelope to break open.

NaCl: the Na+ ion of NaCl creates the ionic bond with the negative charge of DNA and neutralize the DNA. It will help DNA comes together and protect from denaturation.

MgCl2: overall, it protects the DNA. MgCl2 block the negative charge of the lipoproteins of the cell membrane. After the lysis of cell, there is no compartment in the cell hence it protects DNA by mixing with other cell organelles.

Phenol: it precipitates the protein impurities. 

The SDS removes the negative charges from the amino acid and disrupts the confirmation of a protein. Hence the protein losses its structure and stabilized by using the SDS.

The combination of phenol, chloroform and isoamyl alcohol helps in the removal of protein. After centrifugation, the phenol settles in the bottom of the tube and DNA in the aqueous phase while the denatured protein remains between both layers as a whitish cloud.

So care must be taken to collect nucleic acid from this method. The collected nucleic acid is precipitated with the help of chilled alcohol (isoamyl alcohol). We can add salt as well to increase the yield of the DNA. For more detail on the role of alcohol in DNA extraction read our previous article,

Role of alcohol in DNA extraction

Finally, the DNA is dissolved in TE buffer. Because of the use of the organic solvents, this method is also named as an organic solvent-based DNA extraction method.

The PCI method of DNA extraction is widely accepted. Even the forensic departments trust PCI method rather than Kit method. The quantity of DNA obtains by PCI method is very high. We can obtain 800 to 900 ng of DNA with great quality.

If we prepare all chemicals very well and perform it sincerely we can always get a good result by this method.

However, the amount of sample required for PCI DNA extraction is high. It is difficult to isolated DNA from the samples such as hair and nail. Also, the purity of DNA becomes a major issue if not performed well.

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Precipitated DNA

Some of the interesting articles, 

An enzymatic method of DNA extraction:

Actually, this method is a combination of salt and enzyme. Here the extraction buffer is used before going further on enzymatic digestion.

The extraction buffer composition may vary from lab to lab, however, the major components are Tris, EDTA, NaCl, sodium lauryl and SDS. Here phenol, chloroform or isoamyl alcohol is not used. Instead, the enzyme proteinase K is utilized for digesting the sample.

The sample is incubated with proteinase K for 2 hours this will digest all the protein present inside the sample.

Immediately after the proteinase K digestion, the sample is precipitated by chilled alcohol. By centrifuging sample, all other cell debris are removed. Finally, the DNA pellet is dissolved in TE buffer.

This method of DNA extraction is rapid and easy. We can use ready to used DNA extraction buffer. Even the yield is very high. However, the quality of DNA is a major concern in this method.

Silica column based DNA extraction method

The silica column based DNA extraction method is very unique and different from other DNA extraction methods.

In the PCI or proteinase K method we have to centrifuge sample many times and have to collect aqueous phase or pellets depending upon the step of extraction. Sometimes we have to collect aqueous phase or sometimes we have to collect pellets.

The silica-based DNA extraction method works on the unique chemistry of interaction between silica and DNA. A positively charged silica particles bind with the negatively charged DNA and hold it during centrifugation.

The method was first described by McCormick in 1989. However, the idea was developed in 1979, when silica was used in DNA purification by Vogelstein.

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The image represents the general process of Spin column method for DNA extraction.

The silica-based solid phase DNA extraction method is now commercially available and it is most routinely used in diagnostic laboratories. Because of its good quality yield of DNA and simple operating system, it is widely accepted.

The lysis buffer breaks the cell membrane and nuclear envelope. The proteinase K digests all the protein.

In the very first step, the sample is incubated with cell lysis buffer or called as DNA extraction buffer.

Along with it, a small amount of proteinase k is added to the sample. All the other impurities are removed by centrifugation. Here the DNA remains bounded with silica and other impurities passes through the silica column.

Now the DNA can be washed twice for improving the purity of DNA. The aqueous phase contains the impurities are discarded by discarding the collection tube.

Finally, the DNA is dissolved into the TE buffer. The method is fast reliable, accurate and consumes less time as compared to other methods.

DNA extraction by magnetic beads:

Personally, I had never worked with magnetic bead DNA extraction but I know little about the magnetic bead method of DNA extraction. Positively charged magnetic beads attract the negatively charged DNA, finally, the DNA is separated under the magnetic field. In this technique also, we have to use the DNA extraction buffer.

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the graphical representation for comparison of different DNA extraction methods.

My ultimate Guide for DNA extraction

I had worked with all three types of DNA extraction methods Yet, PCI DNA extraction method is one my favourite because only the PCI method gives you the freedom to do something different with your work.

If you are working with ready to use kit, the buffers, spin column tubes and other utilities are provided by kit manufacturer inside the kit, you have to just follow the steps as per the protocol is given. You cannot do something new with that.

Instead, in PCI you can play with the protocol (once you have achieved that expertize). You can do changes to buffer composition, you can use different chemicals, different physical methods etc to enhance your result and that is the beauty of working with PCI.

Nonetheless, care must be taken while performing PCI. The phenol is a volatile organic chemical which can burn your clothes and skin.

Also, the chloroform can be dangerous to health. So you have to be careful while dealing with PCI.

Our PCI protocol is very precise, we got result from using only 20µL of sample. I will give you my DNA extraction protocol of PCI later on in another article. 

Phenol can be oxidized under the sunlight hence always store phenol in a brown coloured umber bottle.

Wear a lab coat, gloves, goggles and mouth cape while performing PCI method of DNA extraction.

In the case of the enzymatic method of DNA extraction, Store proteinase K at 4ºC temperature after reviving it otherwise the activity will reduce over a period of time.

Mixing sample with buffer or chemical is very crucial, don’t take it granted. As you mix the sample well, the purity and quantity of DNA will automatically increase.

DNA extraction step

Chemical

Lysis of cell wall/ cell membrane and Lysis of nuclear membrane

Tris, MgCl2, EDTA, NaCl, SDS, CTAB, Triton X100

Digestion of protein

CTAB, SDS, phenol, chloroform, Nonidet P40, different chaotropic, urea, guanidium isothiocyanate, guanidium thiocyanate, N-Lauroyl sarcosine

Precipitation of DNA

Isopropanol, ethanol, methanol, NaCl, sodium acetate

Washing of DNA

Any alcohol

Dissolving DNA

TE buffer, distil water

Conclusively, we can say that the choice fo DNA extraction method entirely depends on us. So many modifications fo DNA extraction methods are available in the literature. We have to select our own methods from available different types of DNA extraction methods.

I have enlisted different chemicals used in each step, you can choose the appropriate chemical and design your own protocol.

Detailed PCI DNA extraction method, DNA extraction method for plan tissue and for other tissues I will explain you in the next article.

Till then, stay connected with this article.

Comment in the comment box below and contribute to increase the content of this article.

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Article written by: Tushar ChauhanArticle reviewed by: Binal Tailor, Ravi Parmar

Categories: All articles, DNA Extraction, Explore Tags: , , , , ,

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