Posted 28 October 2011 - 11:51 AM
There is a lot of data that suggests freeze thaw, and especially the conditions under which you perform them, can be detrimental to certain proteins. However DNA tends to be fairly robust to freeze thaw. So what may be happening is that by freezing and thawing is destroying loose proteins and proteases and effectively purifying your DNA solution.
The question is while this gives "better" PCR results, is it actually a best practice. There are surprisingly many publications on freeze thaw in general. Ultimately the best answer to all of your questions about DNA, RNA, and cDNA storage is to do a thaw study and confirm what works best in your process.
I do PCR as well. We were getting concentration shifts in bulk oligos. Turns out inconsistent thawing was causing heterogeneity within tubes. When we would aliquot from the tube, the concentration of the tube would then drift. Furthermore, surface tension in the narrow Matrix tubes we stored them in, made it so that even vortexing was not a sufficient remedy. We performed similar studies, found out some things we didn't anticipate, then developed optimized thaw procedures based on that data. It has yielded better process control data (I'm so pumped about it, I'm raising this point in the many threads on the topic).
FYI, we thaw almost everything on Box Scientific thaw stations now. They use ambient air convection to speed up thaw times at room temperature. This way we don't risk heat damage of cDNA and RNA. Also, its a fixed platform like a heat block, so once we found an optimum thaw time we proceduralized it, hence our better reproducibility.
Hope that helps.