In this lab, we are trying to find unique genetic signatures of organisms in sediment samples and from isolated cells. Since we prep a lot of samples, there’s always the chance that DNA from one experiment could wander into the tubes for another. This is a Bad Thing, since we don’t have any way of telling whether a bit of DNA is supposed to be there or not. And since our detection techniques are sensitive, even a tiny amount of contamination can make a big difference.
The best way to deal with this is:
Before you begin any experiment in the PCR or primary-purification areas,
you must perform a Bench Cleanup Protocol.
1. Put on a pair of latex gloves.
2. Remove pipets, pipettors, beakers of tubes, boxes of pipet tips, etc. from the bench surface.
3. Wipe the entire bench surface down with Clorox solution, followed by a wipedown with 70% ethanol. Allow to air dry. The bench surface is now free of all DNA.
4. Wet a Kimwipe with a bit of the Clorox solution. Wipe down the bottoms of the beakers and tip boxes, and place them on the bench. Throw out the Kimwipe.
5. Wet down a Kimwipe with some RNAse AWAY solution. Carefully wipe down all surfaces of each of the pipettors. Clean away the solution with a fresh Kimwipe. Change gloves after cleaning if you have any reason to suspect a pipettor is heavily contaminated with DNA (such as the presence of dried globs of something-or-other). Throw out the Kimwipes, and change gloves.
6. Get a waste container. If you are in the PCR areas, use a fresh, clean 800-ml beaker. If you are in the primary purification room, put a new plastic bag inside the round metal waste container.
7. If there is something that you cannot clean this way, such as some powdered reagents, you can use a short-wave UV light. Ask Andrea to show you how.
You are now ready to begin your experiment.
During the experiment:
After you’re done:
Dispose of your garbage. Do not bring the container (beaker or bag) back into the room.
Do a Bench Cleanup Protocol again. Yes, the next person ought to clean up before
they start. This is an insurance policy. Finding and eliminating a hidden source
of contamination is a royal pain, and we want to avoid it if at all possible.
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