I have been working on LAMP for quite some time now and have realized that DNA contamination in the negative controls is a frequently occurring problem, especially because I have do gel electrophoresis, which means I open the tubes after amplification.
I have tried using UV, sodium hypochlorite, ethanol and IPA treatment on the work surfaces to get rid of the carried over DNA contamination, but that has not been very helpful. I frequently autoclave whatever it is that can be autoclaved prior to setting up a LAMP reaction. Also, the work areas for setting up the reaction and for electrophoresis (where I open the tubes) are separate, even the set of pipettes, tip boxes etc. are isolated for each work area.
However, the problem of carried over DNA contamination has been a persistent issue. I want to know which chemicals are potent in destroying traces of DNA or if there is any other way around this problem that someone knows of.
It would be great if someone could help me this problem. Thanks!
If you can heat up your sample up to 75'C, you could DNaseI treatment (I use QIAGEN DNase set and it works well). The alternative is sth called gDNA wipeout, but this is part of QIAGEN RT-PCR kit, so I am not sure if they sell it on its own. With gDNA wipeout you heat up the sample for 2min, 32'C if I remeber correctly. Question is how much you want to chop up your DNA contaminats. Those enzymatic treatments might not give you single nucleotides only
Hi Pryianka,
in my former lab we cleaned DNA traces using "DNA away" a chemical similar to Exitus DNA, cited by Florian.
UV lights work better when either in proximity to the surface to be cleaned, or used for a long time (at least 20 minutes in a UV crosslinker).
Making aliquotes of the reagents and irradiating them (when possible) can also help reducing contamination.
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