As mentioned earlier, you can use ethanol or isopropanol in precipitating DNA from the solution and get the same end results. However, the solubility of DNA differs in each of these solvent. For the record, DNA is less soluble and falls out of the solution faster even when low concentrations of isopropanol are used but there is a tendency that the salt will co-precipitate with the DNA.On the other hand, a higher concentration of ethanol is needed to precipitate DNA from the solution but then the salts tend to stay soluble, even at lower temperatures.
So, which solvent should you use? Well, this may depend on the volume of the sample you need to precipitate. As a general rule, you should use ethanol if you are only precipitating small volumes of DNA. This way, you can recover larger volumes of DNA without worrying about salt contamination as you would when you choose to use isopropanol. You should also use ethanol if your sample will be stored for long periods of time under low temperatures.
Isopropanol should be used when working with larger samples since you would only need a small amount of the solvent. However, you need to precipitate with minimal incubation time and carry it out at room temperature to minimize salt precipitation.
