DMSO usage

[spal]

I have been routinely using 5% DMSO for cpDNA amplification and have had much success with many of my DNA samples. I understand that DMSO's utility is greatest with GC rich regions. However, because DMSO has improved amplification yield, my default is now to use DMSO with all of my PCR reactions.

Are there any reasons why I should not default to DMSO use (regardless of GC content of the template?)

[sosaidellie]

DMSO can reduce the efficiency of your PCR because it chelates magnesium and so inhibits the polymerase activity. I remember reading somewhere though that as long as you make sure there is more magnesium than DMSO you should be ok.

Personally, unless you are concerned about secondary structure formation causing non-specific amplification (or no amplification), I wouldn't bother with DMSO.
My target gene is has extremely low abundance, but I get an ok yield using seminested PCR without DMSO. That's probably a more time consuming way to increase yield but we are concerned more with fidelity, and the seminested allows us to minimise the number of cycles needed. I guess it depends what you want to use the product for in the end.

Hope this helps

[pigfarmer]

I used to do that as well, but then I stopped running PCR with DMSO and I got the same results. Now I only use it for those that I really need it to make the PCR work. However, to answer your question, I really don't think you should worry about it if your PCR works, "if it ain't broke, don't fix it!"