why ethanol is used in gel electrophoresis
Answers
People precipitate DNA with ethanol and run it on a gel all the time. What you describe sounds a little atypical, but I'm not sure what sort of sample you are starting with. Things to keep in mind 1) After initially precipitating DNA in 100% EtOH, washes should be done in 70% EtOH 2) DNA pellets are usually tiny and I would avoid moving them between tubes if possible. Its best to combine all your DNA when it's still in aqueous solution, add the EtOH (and salt if needed), and then spin. Keep the pellet in this tube for one or two additional washes 3) At the end, remove all the liquid you can and then air dry the pellet. I usually do this for 10 to 15 minutes 4) Last, you need to get the DNA back in solution by adding TE or water to the pellet. For small amounts of DNA, you can immediately pipet to get the DNA resuspended. Then you can combine some of this with loading dye and run it on a gel. If you don't get rid of most of the EtOH, the sample won't sink into the wells