Has anyone worked in a molecular biology lab which is ventilated inside the lab? We have a lab originally designed for sterile area. And now it is intended to be used as a molecular biology lab. I am pretty worried whether this may cause contamination of PCR etc. . As a molecular biology lab the air should be able to go outside of the lab, at least some part of the room air if not 100%.
This lab is for sterile work, thus the whole lab is inter ventilated meaning the air circulate inside the rooms even though passing through filters again and again. So, my second questions is can the filters can also get rid of DNA molecules from the air? If this is true, then maybe I shouldn't be worrying too much of this.
It all depends on the kind of molecular biology & PCR experiments you want to perform. If you wish to use PCR to detect DNA sequences present in minute amounts (e.g. for forensic investigations), then contamination is a big issue. If you plan to "PCR out" a specific gene from genomic DNA in order to clone it, you probably don't need to bother because amplification will be specific for your gene if you choose the primers properly
PCR contamination is a huge issue. This video https://www.youtube.com/watch?v=0BuRECUOsx0 discusses it a little bit. In many fields of research we know when things are contaminated, but in some fields a lot of contamination goes undetected.
It all depends on the kind of molecular biology & PCR experiments you want to perform. If you wish to use PCR to detect DNA sequences present in minute amounts (e.g. for forensic investigations), then contamination is a big issue. If you plan to "PCR out" a specific gene from genomic DNA in order to clone it, you probably don't need to bother because amplification will be specific for your gene if you choose the primers properly
Contamination creates problems in cases other than rare DNA from ancient bones and other cases of "rare DNA". It can also raise havok with studies of population biology and species identification (DNA barcoding) etc. The ultra clean room steps taken to ensure lack of contamination in some studies of ancient DNA are not always necessary for other types of studies, but many of the "sterile procedure" steps taken to work with cell cultures are not quite sufficient to prevent PCR contamination events. Even if the HEPA filter in a fume hood venting directly back into the lab is not likely to be the major source of a problem, there are many other things to consider such as never using a Pipettman for handling sample set-up that has previously been used for PCR product work. Many groups maintain separate rooms for sample prep work and never allow PCR product to get anywhere near the sample prep room.
As Pierre has suggested above, unless you are performing procedures such as those described by Brian above where contamination with even one copy of a sequence could render an experiment unusable, sometimes it is possible to over-think the problem. 25 years ago when I was learning PCR, we were trained to UV treat everything, surfaces were wiped down with "DNAaway (tm)", most reagents were pre-aliquoted by the lab senior post-doc in a space away from the main lab and used a minimal number of times only and so forth. Always discard any reagents or reactions when there is any doubt etc.. Over time I got much quicker and more relaxed at setting up PCRs, and in the space of 25 years I can count on the fingers of one hand the times when I've experienced contamination.
The one situation where I would be genuinely concerned about the ventilation situation is if you are handling large volumes of liquid (bacterial cultures containing plasmid etc.) - in this situation if there is a spill, the recirculating nature could lead to endemic contamination of the atmosphere with template. There will be many of us who remember stories from the late 80s / early 90s of labs continually PCR-cloning mutant versions of v-myc or p53 etc. "out of the atmosphere" that could be traced back to broken flasks or lab accidents 10 years previously.
The most important thing is having adequate controls and readouts that can separate genuine results from contamination, and if things go really pear-shaped, already have a plan of action regarding who you can pin the blame to. (yes - that might be a joke!).
Best of luck!
Many thanks to everyone of you for kind help. I will anyway set-up the PCR reactions with current ventilation. With answers from you guys, I feel better to continue, being not worrying so much, but of course will be careful with enough controlls un along. Thanks again ! :D
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