The Effects of DMSO on DNA Conformations and Mechanics

Dimethyl sulfoxide (DMSO) is a polar aprotic solvent used in a wide range of applications, including uses as a drug and in drug delivery, as a solvent for fluorescent dyes, and in enzymatic reactions that process DNA. Consequently, many assays contain low concentrations (≤10%) of DMSO. While it is well known that DMSO lowers the melting temperature of DNA, its effects on DNA conformations and mechanical properties below the melting temperature are unclear. Here, we use complementary single-molecule techniques to probe DNA in the presence of 0–60% DMSO. Magnetic tweezers force-extension measurements find that the bending persistence length of DNA decreases moderately and linearly with DMSO concentrations up to 20 vol %, by (0.43 ± 0.02%) per %-DMSO. Magnetic tweezers twist measurements demonstrate a reduction in melting torque in the presence of DMSO and find that the helical twist of DNA remains largely unchanged up to 20% DMSO, while even higher concentrations slightly unwind the helix. Using AFM imaging, we find a moderate compaction of DNA conformations by DMSO and observe a systematic decrease of the mean-squared end-to-end distance by 1.2% per %-DMSO. We use coarse-grained Monte Carlo simulations of DNA as a semiflexible polymer with a variable density of flexible segments, representing DMSO-induced local defects or melting, to rationalize the observed behavior. The model quantitates the effects of introducing locally flexible regions into DNA and gives trends in line with the magnetic tweezers and AFM imaging experiments. Our results show that addition of up to 50% DMSO has a gradual effect on DNA structure and mechanics and that, for low concentrations (≤20%), the induced changes are relatively minor. Our work provides a baseline to understand and model the effects of DMSO on DNA in a range of biophysical and biochemical assays.