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[DESCRIPTION]
The traditional phenol extraction procedure, based on early work by Kirby (1957) and elaborated in most modern protocol compendia, yields very clean nucleic acids suitable for a variety of downstream applications. This extraction method is coupled with a routine alcohol precipitation step to allow buffer exchange, removal of trace amounts of chloroform, and concentration of nucleic acids (Sambrook and Russell 2001).<br /><br />This is a protocol from: <br /><br />Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7<br /><br />Please see the <a href="http://www.aslo.org/books/mave/MAVE_154.pdf" target="_blank">published manuscript</a> for additional information.

[GUIDELINES]
<strong>Materials and equipment:</strong> <br />• fume hood <br />• microcentrifuge (refrigerated if possible) <br />• pipettes and sterile, disposable tips <br />• safety gear (gloves, lab coat, safety glasses) <br />• sterile microcentrifuge tubes <br />• TE buffer (10 mM Tris, 1 mM EDTA; pH 8) <br />• Tris-saturated phenol, pH 8 (<em>see</em> “Warning” below) <br />• CI (chloroform:IAA, 24:1, vol:vol) (<em>see</em> “Warning”) <br />• PCI (phenol:chloroform:IAA, 25:24:1) (<em>see</em> “Warning”) <br />• sodium acetate, 3 M, pH 5.2 (<em>see</em> Sambrook and Russell [2001] for a discussion of alternative salts that may be used for nucleic acid precipitation and their advantages and disadvantages) <br />• Optional: polyacryl carrier (Molecular Research Center) <br />• ethanol, 70% and 100%<br /><br /><strong>Warning:</strong> Phenol can cause chemical burns if it comes in contact with bare skin. Phenol and chloroform are volatile and carcinogenic and must be used in a fume hood with proper protection (gloves, lab coat, and safety glasses). PCI and CI preparations that are ready to use can be purchased from a variety of scientific chemical suppliers. Details of how to prepare these solutions for oneself can be found elsewhere (Sambrook and Russell 2001).<br /><br /><strong>Assessment:</strong> This traditional method of extraction is most commonly used to extract DNA. When phenol is saturated with alkaline buffer (e.g., Tris, pH 8), however, both RNA and DNA will partition to the aqueous phase, so the method can be used for total nucleic acid extraction. Either DNA or RNA can be specifically selected by digestion of the recovered total nucleic acids with RNase or DNase. If targeting RNA, an RNase inhibitor may be included to help ensure stability. If one wishes to isolate both RNA and DNA but in separate fractions by organic extraction, we recommend the use of the commercially available reagents TRI Reagent and TRIzol (see above). <br />     Although still in use, the popularity of organic extraction has waned somewhat as new extraction procedures have been developed that do not require the use of toxic organic compounds. In addition to the extra precautions that must be taken when handling phenol and chloroform during extraction, the disposal of the resulting organic waste is costly.

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