Phenol extraction is a widely used method for extracting pure DNA and RNA from cell samples. Phenol is introduced to the sample, attracting proteins and breaking them down, while leaving DNA and RNA intact. The mixture is then separated and the DNA or RNA is extracted from the water phase. The acidity of the mixture is important for efficient extraction.
Phenol extraction is a scientific process of extracting pure ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) from a specific cell sample. The process mainly consists of separating or removing proteins from the cell, leaving behind the DNA and RNA. Worldwide, phenol extraction is the most widely used method for extracting pure samples of DNA and RNA.
The phenol extraction process begins when the chemical compound phenol is introduced into the cell sample which is usually found in a water mixture. Just like oil, phenol’s chemical structure doesn’t allow it to mix easily with water, so it will just sink under water, since phenol is denser. The chemists would then mix the two phases, water and phenol, to temporarily create an emulsion.
While the phenol is within the aqueous layer, it will attract the protein elements of the cell sample and break them down. The DNA or RNA, meanwhile, will remain intact within the aqueous phase. Then, the container of the entire mixture will be placed inside a machine called a centrifuge, which will help separate the mixture into its two original phases, phenol and water. Once the mixture is separated, the chemists would extract the water containing the DNA or RNA, while the phenolic phase is removed. The DNA undergoes further precipitation with ethanol to “desalinate” it and make it more concentrated.
The choice of phenol for DNA extraction occurs because the compound is a non-polar molecule, whereas both DNA and water are composed of polar molecules. In chemistry, the general rule is that polar molecules dissolve better in polar molecules and non-polar molecules can easily dissolve non-polar molecules. This means that while phenol dissolves protein during phenol extraction, it will not dissolve DNA or RNA, so they retain their structure and can be extracted from water. Phenol is so good at dissolving proteins that the proteins will be broken down permanently.
In a phenolic extraction, the acidity of the entire mixture is important to efficiently extract the DNA and RNA. Chemists recommend that the phenol have a pH above 7 so that the water layer can successfully collect the DNA. At a pH of 4.5, which is already considered acidic, RNA can already be harvested from the aqueous phase. To change the acidity or alkalinity of phenol, certain chemicals are added, such as the tris compound or N-ethylmorpholine.
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