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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

Note: phenol-chloroform is stored at 4 °C