Phenol extraction is a commonly used method for removing proteins from a DNA sample, e.g. to remove proteins from cell lysate during genomic DNA preparation.

Organic extraction involves the addition of and incubation in multiple different chemical solutions; including a lysis step, a phenol chloroform extraction, an ethanol precipitation, and washing steps.

Samples are homogenized in a phenol-containing solution and then centrifuged after chloroform addition. During centrifugation, the sample separates into three phases: an upper aqueous phase which contains DNA, an interface containing the proteins, and a lower organic phase containing RNA and lipids.

The advantage of the phenol-chloroform method is the simplicity of the protocol, the rapid denaturation of nucleases and the stabilization of nucleic acids. The main disadvantage is the use of toxic chemicals phenol and chloroform, and there is an increased risk of contamination due to transferring the DNA between multiple tubes.