DMSO is a complex solvent and has many affects on physiological systems. Many articles that use DMSO (for many purposes) show solvent effects compared to non-exposed controls. Personally I would avoid it and look for an alternative. Alterantively, spend some time investigating how DMSO affects your system (dose-response curves) before adding your drugs, and determine the lowest concentration needed to solubilise your drugs for testing. See as one recent example:

Diverse effects of dimethyl sulfoxide (DMSO) on the differentiation potential of human embryonic stem cells

by Pal, R et al., 2012 in ARCHIVES OF TOXICOLOGY Volume: 86 Issue: 4 Pages: 651-661 DOI: 10.1007/s00204-011-0782-2 Abstract: In vitro disease modeling using pluripotent stem cells can be a fast track screening tool for toxicological testing of candidate drug molecules. Dimethyl sulfoxide (DMSO) is one of the most commonly used solvents in drug screening. In the present investigation, we exposed 14- to 21-day-old embryoid bodies (EBs) to three different concentrations of DMSO [0.01% (low dose), 0.1% (medium dose) and 1.0% (high dose)] to identify the safest dose that could effectively be used as solvent. We found that DMSO treatment substantially altered the morphology and attachment of cells in concurrence with a significant reduction in cell viability in a dose-dependent manner. Gene expression studies revealed a selective downregulation of key markers associated with stemness (Oct-4, Sox-2, Nanog and Rex-1); ectoderm (Nestin, TuJ1, NEFH and Keratin-15); mesoderm (HAND-1, MEF-2C, GATA-4 and cardiac-actin); and endoderm (SOX-17, HNF-3 beta, GATA-6 and albumin), indicating an aberrant and untimely differentiation trajectory. Furthermore, immunocytochemistry, flow cytometry and histological analyses demonstrated substantial decrease in the levels of albumin and CK-18 proteins coupled with a massive reduction in the number of cells positive for PAS staining, implicating reduced deposits of glycogen. Our study advocates for the first time that DMSO exposure not only affects the phenotypic characteristics but also induces significant alteration in gene expression, protein content and functionality of the differentiated hepatic cells. Overall, our experiments warrant that hESC-based assays can provide timely alerts about the outcome of widespread applications of DMSO as drug solvent, cryoprotectant and differentiating agent.

What are your controls? - assuming that each of the drugs will be compared to the cells treated with MeOH and DMSO of the same concentration, respectively.

Either alone could most definitely have an effect on gene expression...

DMSO is toxic to some cells, so it there is definitely a possibility that it may be effecting your gene expression.

in similar experiments I found out that DMSO induced ATP production and proliferation esp at doses of 0.2% and above. i avoided the problem by using < 0.2% DMSO as my vehicle controls. its always better to use low concentrations of drugs to be tested. skip the higher doses and focus on the lower ones.

Alternatively, you can serum starve your cells (2% FCS in complete media) overnight before you begin the treatment, that would make cells fall to a quiescent state and you might see desirable results.

Thanks all.

I know the exactly taht Larissa tolds you. At low concentration, DMSO can act as an antioxidant, but be carefull ..no more that 0,25%

DMSO is a complex solvent and has many affects on physiological systems. Many articles that use DMSO (for many purposes) show solvent effects compared to non-exposed controls. Personally I would avoid it and look for an alternative. Alterantively, spend some time investigating how DMSO affects your system (dose-response curves) before adding your drugs, and determine the lowest concentration needed to solubilise your drugs for testing. See as one recent example:

Diverse effects of dimethyl sulfoxide (DMSO) on the differentiation potential of human embryonic stem cells

by Pal, R et al., 2012 in ARCHIVES OF TOXICOLOGY Volume: 86 Issue: 4 Pages: 651-661 DOI: 10.1007/s00204-011-0782-2 Abstract: In vitro disease modeling using pluripotent stem cells can be a fast track screening tool for toxicological testing of candidate drug molecules. Dimethyl sulfoxide (DMSO) is one of the most commonly used solvents in drug screening. In the present investigation, we exposed 14- to 21-day-old embryoid bodies (EBs) to three different concentrations of DMSO [0.01% (low dose), 0.1% (medium dose) and 1.0% (high dose)] to identify the safest dose that could effectively be used as solvent. We found that DMSO treatment substantially altered the morphology and attachment of cells in concurrence with a significant reduction in cell viability in a dose-dependent manner. Gene expression studies revealed a selective downregulation of key markers associated with stemness (Oct-4, Sox-2, Nanog and Rex-1); ectoderm (Nestin, TuJ1, NEFH and Keratin-15); mesoderm (HAND-1, MEF-2C, GATA-4 and cardiac-actin); and endoderm (SOX-17, HNF-3 beta, GATA-6 and albumin), indicating an aberrant and untimely differentiation trajectory. Furthermore, immunocytochemistry, flow cytometry and histological analyses demonstrated substantial decrease in the levels of albumin and CK-18 proteins coupled with a massive reduction in the number of cells positive for PAS staining, implicating reduced deposits of glycogen. Our study advocates for the first time that DMSO exposure not only affects the phenotypic characteristics but also induces significant alteration in gene expression, protein content and functionality of the differentiated hepatic cells. Overall, our experiments warrant that hESC-based assays can provide timely alerts about the outcome of widespread applications of DMSO as drug solvent, cryoprotectant and differentiating agent.

I also would like to add to what been mentioned , that DMSO mustn't be added at room temperature, rather at 5 degrees celsus , as it deteriorate the cell proteins resulting in a sudden death to the cell. I still realy don't have a sceintific explanation why the solvent high temperature harm the the protein, and why it does a good job at chilling degrees???. best wishes in your research

As long as the final concentration of DMSO in your solution is less than 0.05%, you should be ok. I routinely use samples of human primary cells treated with a drug dissolved in DMSO, use them for all sorts of downstream applications , and never see an effect from my vehicle control.

I agree with Faezeh. But some kinds of cells may be very sensitive to DMSO, to exclude this, you can adopt a control without DMSO. If there are still significant influence on your cells when you reduce the concentration of DMSO to less than 0.05%, you might have to change a solvent.

Dear Xiaojin Liu thanks for your comment. I agree with you and I have to test your idea and then change my solvent.

I agree with Dr  Edwin J Routledge about affects of DMSO on cultured cells. I examined affects of 1%DMSO on expression of house keeping gens in HepG2 cells and THP-1 macrophages. In this case we could not find certain changes in the gene expressions. But on moderate expressive genes the expressions are decreased largely. 

Thank you guys, I understand why i saw a morphological effect with my DMSO control, really did not expect to see any change with it. Makes my small project more interesting now.