Cells form membraneless organelles, which definea separate liquid phase, made out of protein chains. These regions are by their dielectric constant similar to organic solvents such as acetonitrile and DMSO. In these organelles DNA double helix can unwind, while structures from single-stranded nucleic acids become stabilized. In this work we used organic solvents to mimic the dielectricity of environment inside membraneless organelles and observed the effect on DNA secondary structure. We used 17-mer complementary DNA chains. NMR spectroscopy was used to observe the effect on hydrogen bonds within the DNA double helix.
We showed that both DMSO and acetonitrile destabilize DNA double helix. DMSO unfolds the DNA double helix at lower volumetric percentage in comparison to acetonitrile. In 50% (v/v) DMSO/water, complementary 17-mer DNA chains still interact, but are not folded into a stable DNA double helix. In 50% (v/v) acetonitrile/water DNA still folds into a double helix, while at 75% there are no stable interactions between the strands. We confirmed that in DMSO/water mixture G-C base pairs are more stable than A-T base pairs. Dielectricity is not the reason for DNA destabilizationin DMSO/water or acetonitrile/water mixtures, key factor for DNA stability in our model system must be found elsewhere.
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