The Protein Man's Blog | A Discussion of Protein Research

Question:

How Genomic DNA extraction works?

The Protein Man Says:

Genomic DNA Extraction Protocols

As mentioned in our previous post, there are a lot of ways by which you can separate your genomic DNA from your sample. Here are some of the most commonly used methods that you can use in extracting genomic DNA from your cell lysate.

• NaOH extraction. Known as the "quick-and-dirty" method of preparing DNA, this technique is quite easy to implement and is usually sufficient for most applications. All you need to do is to incubate your cell lysate at high temperatures or subject it to proteinase K digestion and you can have your genomic DNA ready for downstream applications. However, since DNA extracted using this method may contain high levels of contamination, it should not be stored for future use.
• Phenol-chloroform extraction. This technique uses organic solvents to extract contaminants from your lysate while the DNA is recovered from the aqueous phase through alcohol precipitation. This may be the most conventional technique of extracting highly purified genomic DNA from a sample but it can also be quite time consuming and may not give reproducible yields. 
• Silica-based methods. Genomic DNA can easily be extracted from mammalian cells and tissues as well as from mouse tail, E. coli cells and yeast by using silica-based methods. By choosing to use this genomic DNA extraction protocol, you can get your ready-to-use DNA in less than 15 minutes using a spin column based centrifugation procedure. The extracted DNA using this method has an average size of 20 to 30 kb and is ideal for use in PCR, southern blotting analysis and restriction enzyme digestion.
• Cesium chloride density gradients. Genomic DNA can also be extracted based on density. In this method, the cells are first lysed with an appropriate detergent, mixed with cesium chloride and ethidium bromide and centrifuged at very high speeds for several hours. The resulting DNA band is collected and extracted using isopropanol to remove the ethidium bromide component. Ethanol is then used to recover the DNA. While this method extracts high quality DNA from your lysate, the process is both time and labor intensive and is rather expensive since it requires an ultracentrifuge.