DMSO in PCR - (Jul/27/2008 )
I just wondering while I'm doing PCR for beta-thalassemia mutation detections and my friend doing for alpha-thalassemia. I saw that she use DMSO solution in the PCR mix while I'm told it's not necessary to add DMSO in mine. When I ask her, she said that alpha-globin gene contains a relatively high G-C content compared to beta-globin, so DMSO is used in order to ease the two strands separation in the PCR.
When I read about DMSO in Wikipedia, it's said that addition of DMSO is used in PCR to prevent 2nd stucture formation of DNA but it increases DNA mutation rate (which I conclude will give wrong base pairing during cycles). My question is, what is the real function of DMSO addition in PCR mix? and if it increases mutation rate in DNA, how is the mechanism?
One mechanism that I can imagine is that DMSO is a relatively weak acid, so it readily destabilizes DNA by disturbing purine-deoxyribose bond, yielding apurinic acid. Is it true?
IMHO, I think DMSO effects has more to do with disruption of hydrogen bonding between water molecules and DNA. The effects of DMSO's acidity is low considering the PCR buffer is buffered and amount of DMSO used is quite low.
I would start with Mg++ and K+ optimisation, and then go for other, more exotic, components.
My question is, what is the real function of DMSO addition in PCR mix? and if it increases mutation rate in DNA, how is the mechanism?
Increased mutation rate from DMSO is probably a side-effect of the reduced H-bonding pernesblue mentioned. Less-stable base mismatched are allowed, so unless the polymerase is a good proof reader, the chance of a mismatch is higher.
other higher structure disrupting options that are more friendly on your are the ENHANCER that comes with Invitrogen's Taq Platinum (red lid) or betaine. I use 0.5 uL for a 25 uL reaction.