Smolke:Protocols/DNA purification

Situations to use a column-based purification kit

 * Cleaning up PCR products after each step in assembly PCR. --YC
 * Cleaning up reverse transcription products during SELEX. --YC
 * When I'm in an absolute time crunch, which is not often. --YC
 * Beware the size of you products and whether it's double-stranded or not. I don't have much luck purifying RT products if it's close to 100bp long. --JL

Situations to use phenol-chloroform extraction & ethanol precipitation

 * Cleaning up and concentrating PCR-amplified inserts for cloning. --YC
 * Cleaning up after digestion. --YC
 * You could also just do ethanol precipitation without phenol-chloroform extraction if you are simply trying to reduce the volume of a sample (for subsequent gel extraction, for example). I believe some people also just put it in the speed vac for this purpose. --YC
 * Large quantities of DNA (>10ug). -JKM