Don't let your DNA sample float away when loading an agarose gel (page 2 of 2)

re-purify the sample using a QIAquick-, or MinElute column, or QIAEX II resin
incubate the eluate at 56C for 10 min to evaporate the ethanol
dry down the sample in a vacuum centrifuge, and resuspend the pellet in a small volume of sterile water

Thanks for the wisdom Qiagen, but MY SAMPLE IS GONE, IT FLOATED AWAY! Of course you could follow their tips with every purified sample you plan to run on a gel, but what was the point of using a kit if it takes longer than old-fashioned methods like EtOH precipitation.

Don't let your sample float away - preventative measures

These tips won't cure the problem with Qiagen columns, but they should help prevent it. First if you are using a vacuum-based approach to clean your DNA, you need a strong vacuum (you can measure it with a vacuum gauge, Qiagen sells them, the desired suction strength is detailed in the Qiagen manual). And you need to vacuum for a long time (at least 5 minutes). To be safer, I'd recommend removing the samples from the vacuum and spinning them for 1 minute at 13K rpm like in the spin column approach instead of a 5 minute final vacuum (my girlfriend taught me this trick). Using the vacuum through the initial steps will still allow you move through the initial purification quickly, while the final column drying spin does a much better, quicker job than the vacuum.

Second, if you've frozen your sample at -20C but the sample is liquid when you take it out of the freezer (or if it thaws quicker than usual for the particular volume of sample), you probably have EtOH in your sample and you should follow one of Qiagen's suggestions from their FAQ 205.

Third, if you are not using a kit, but are using EtOH precipitation, make sure you remove all drops of EtOH from the sides and bottom of the tube with a vacuum. Then leave the tube open for 5-7 minutes to let the trace amounts of EtOH evaporate. If you can see EtOH, you have not vacuumed sufficiently - suck it out.

For completeness, beginner mistakes

Another way your sample will diffuse out is if you load it into the well too quickly; the momentum of your quickly moving air-displaced sample will cause it to hit the bottom of the well and bounce back out into the buffer. To eliminate this problem, load the gel slowly, and never fill the well more than 75% full. It also helps to use a smaller volume pipettor - it is much easier to load a 20 ul sample using a 10 ul pipettor two times than with a 20 ul pipettor one time, because with a 10 ul pipettor your thumb must move a greater distance to move the same amount of air, so it is easier to control how slowly the sample comes out. Once you get used to loading gels, you'll probably be able to use effectively whatever pipettor you like.

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