how DMSO works - (Apr/28/2008 )

Hi was wondering how DMSO reduce/prevent secondary structures in both template and primers.
THanks!

I guess it disrupts base pairing bw nt

I agree to genz,DMSO is used in the PCR reaction to inhibit secondary structures in the DNA template or the DNA primers. It is added to the PCR mix before reacting, where it interferes with the self-complementarity of the DNA, allowing otherwise troublesome reactions to occur.

DMSO disrupts the hydrogen bonds in DNA. This reduces the strength of any secondary structures that form in the template (and primers) allowing the polymerase to read through the region instead of getting stuck before the secondary structure. If you're using DMSO for this purpose, also look at using a reagent called betaine or glycine betaine as it is also called. It performs a similar function to DMSO but is an isostabilsing agent, meaning that it disrupts secondary structure by equalising the strength of GC and AT bonds rather than infering with the bonds like DMSO does. Betaine is much better at dissolving secondary structure than DMSO, so if you try DMSO and it doesn't work try betaine and it probably will. Use a stock solution of 5M and working concentration of 0.5 - 2.0M.

Good luck, Rob