What is DNA extraction & how it works?

Written by: Nermin Đuzić, M.Sc. in Genetics, Content Specialist

Scientist Friedrich Miescher performed the first DNA isolation or extraction experiment in early 1869. Since then, DNA extraction has become the essential tool of molecular biology and genetics and applied fields like forensics, medical diagnostics, and agriculture [1]. Later, in 1958 Meselson and Stahl developed the first protocol for DNA extraction from bacterium E. coli [2]. 

Simply said, DNA extraction is a routine method used to isolate  DNA from the cell’s nucleus or mitochondria [3]. Before we dig deeper into the procedure of DNA extraction, let’s first briefly recall the basic cell structure (Figure 1).

The cell consists of a cell wall/cell membrane and cytoplasm, where several cell organelles are located (mitochondria, ribosomes, nucleus, etc.). DNA location is the nucleus that is surrounded by its nuclear membrane and there is also a small chunk of DNA located in mitochondria. 

To isolate DNA, we have to break down both cell and nuclear membranes. Then we have to remove cell debris. The final step will be to precipitate and purify DNA. DNA extraction consists of three stages [3]:

1. Breakdown (or so-called lysis) of cell and nuclear membrane that is achieved by adding detergents.
2. Removal of cell debris and proteins is done by adding proteases. Proteases are enzymes that digest proteins.
3. DNA purification and precipitation are done by adding ice-cold alcohol ethanol or isopropanol. 

DNA can be isolated from any living organism using many different methods that require various chemicals. Which method to use depends on the sample type and DNA purity and yield required. For example, scientists would use different methods to isolate DNA from plant cells and blood. 

Now, we will be a bit more technical. All DNA extraction protocols can be divided into two main groups comprising of many other techniques:

1. Chemical-based DNA extraction method (solution-based methods)
1. Organic DNA extraction methods
1. Phenol-chloroform DNA extraction method
2. Inorganic DNA extraction methods
1. Proteinase K DNA extraction method
2. Salting-out method
2. Solid-phase DNA extraction method (physical method)
1. Magnetic bead DNA extraction method
2. Paper DNA extraction method
3. Silica-column based extraction method

Chemical or solution-based methods utilize many various chemicals. Based on the type of solvent used, methods can be divided into organic and inorganic. Organic methods use phenol or chloroform as a solvent. Inorganic methods use proteinase K or salts such as sodium chloride, potassium acetate, or ammonium acetate.

Solid-phase DNA extraction methods rely on the unique chemistry of solid/liquid phase DNA extraction. In a technique that uses magnetic beads, the magnetic field separates DNA. Positively charged magnetic beads attract negatively charged DNA. DNA is then washed and separated from the beads. 

Additionally, DNA can be extracted using filter papers or silica, a solid substance that binds DNA and aids in purification. We will explain the silica-column-based method in more detail later below.

Although they are all different, each of these methods undergoes some common steps, as explained above.

Scientists may either buy ready-to-use DNA extraction or develop and rely on their own DNA extraction methods. At BioCertica, we rely on the silica-column extraction method, and we will explain it in the next section.

How does DNA extraction work?

The previous article explained how our customers collect saliva samples and send them for analysis. Once we receive the sample, we examine it for damage or inadequate sampling. 

If everything is in order, the sample is ready for DNA extraction using a silica-membrane-based method. The method is carried as follows:

• Extraction starts by adding a lysis buffer to the sample to burst the saliva cell membrane. At the same time, we add an enzyme protease to break down the proteins. This step is necessary to release the DNA from the sample. 
• The first step also includes keeping the sample in a hot tube at 37° C. The sample should be occasionally mixed at high speed (in science known as vortexing).  The purpose of this is that the lysis buffer and enzyme have maximum effect. 
• The next step is to add highly concentrated alcohol followed by vortexing. This step helps the DNA aggregate and precipitate from the other particles in the sample (cellular debris and proteins). 
• The sample is then transferred into a silica-membrane column tube and heavily centrifuged (rotated at very high speed). This separates fluids and particles of different densities. During this step, the heavy parts (cell membranes, proteins, and other particles) are sedimented through the membrane and accumulated at the bottom of the column tube. At the same time, DNA is "caught" on the silica membrane within the column tube. 
• This is followed by a series of washing steps to obtain a high-quality DNA sample. The completely extracted DNA is retrieved from the membrane tube using an elution buffer.
• DNA is then ready for quality control checking and preparing for genotyping. But more about that in the next article. 

We can conclude that DNA extraction is a simple procedure that can be performed even in your kitchen using household materials. Don’t you believe it? Then watch this short and simple video that explains how you can extract DNA from bananas.

References

1. Tan, S. C., & Yiap, B. C. (2009). DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology, 2009.
2. Meselson, M., & Stahl, F. W. (1958). The replication of DNA in Escherichia coli. Proceedings of the national academy of sciences, 44(7), 671-682.
3. Alonso, A. (2013). DNA Extraction and Quantification. Encyclopedia of Forensic Sciences (Second Edition). 214-218