Oxirane
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DNA decontamination
I was thinking of ways to decontaminate any traces of DNA and have done some research on the subject. It must be decontaminated to the extent that it
will not contaminate PCR.
I have not found the decomposition temperature of DNA so far. It will denature, or melt, at 60-70C, but this temperature is definitely not to render
it obsolete. So how much temperature there should be? 100C? 200C? I'll bet my mother's kidneys for that it will be permanently destroyed at conditions
like blasting a torch on it, but just how much is needed?
Other ways that will work are bleach(sodium hypochlorite) in general at 5-10% concentration, and UVC light source. Sodium hydroxide solutions should
also do the job, but not sure at what concentrations and temperatures at minimum. These may not be available for all surfaces though, so I'd be very
interested wether for ex. putting the items into oven heated to specific temperature would do the job?
[Edited on 10-10-2014 by Oxirane]
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Chemosynthesis
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Over 190C dry heat. http://www.ncbi.nlm.nih.gov/m/pubmed/23621849/
Compare that to PCR's typical heat block denaturing step (95C for 2-4 minutes) and you'll find 100C isn't nearly enough
I wouldn't trust hydroxide without some more research on time of exposure; it's used in alkaline hydrolysis and midiprep, where it lyses cells,
hydrolyzes RNA, but only denatures most DNA. If I remember correctly that is up around 0.2N concentration. Hypochlorite may be mechanistically more
effective due to chloramination, but I am just speculating and would need to look into that, but not at this hour.
Edit: lied and looked it up now anyway. It appears my speculation is founded
http://www.ncbi.nlm.nih.gov/m/pubmed/11800600/
[Edited on 13-10-2014 by Chemosynthesis]
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Oxirane
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Thanks for info.  I was thinking of blasting the temp-standing parts with propane
torch, it would generate sufficient heat to completely decompose any traces.
I found this document, which compares many different methods. Here they state that concentrated sodium hydroxide is effective at destroying DNA as
well:
http://public.wsu.edu/~bmkemp/publications/pubs/Kemp_and_Smi...
I was originally thinking of soaking all the parts in heated(60-90C) strong(50%) NaOH solution for 5 minutes or so. It looks that this method should
provide good results, because NaOH will also eat away any organic residues left on the equipment and degrease them.
[Edited on 14-10-2014 by Oxirane]
[Edited on 14-10-2014 by Oxirane]
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Chemosynthesis
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No problem. Hope it was helpful, and sorry I didn't see this sooner. Very interesting, I am curious where you end up with this. What exactly are you
cleaning, by the way?
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Oxirane
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I have recently interested in biochemistry and DNA research and I was thinking of how to manage the whole setup. Its just essentially all the equipment that comes into contact with different steps, like containers, pipettes and
other stuff.
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Chemosynthesis
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Ah. Too bad autoclaves don't come with the kitchen sink.
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Sniffity
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If you want to decontaminate DNA, you really need a way to assess contamination.
Running nano spectrophotometry on DNA samples, at 230, 260, 280 and 320 nm is the usual method.
The method of decontamination will depend on the readings you get, meaning on what your impurities are. For instance: Too many proteins, use more
proteinase K. Etc.
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Tsjerk
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Usually people working with PCR only worry about DNAses, not DNA contamination. As long as you wash with a detergent and don't spit in your sample you
should be fine.
DNAses can be inactivated by autoclaving. That is what we do in the lab, just autoclave equipment and water. Works perfectly fine as long as you are
not doing some super sensitive forensic PCR work on the only cell found on the scene of a murder.
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