Double-Stranded DNA Dissociates into Single Strands When Dragged into a Poor Solvent

DNA displays a richness of biologically relevant supramolecular structures, which depend on
both sequence and ambient conditions. The effect of dragging double-stranded DNA (dsDNA) from water
into poor solvent on the double-stranded structure is still unclear because of condensation. Here, we
employed single molecule techniques based on atomic force microscopy and molecular dynamics (MD)
simulations to investigate the change in structure and mechanics of DNA during the ambient change. We
found that the two strands are split apart when the dsDNA is pulled at one strand from water into a poor
solvent. The findings were corroborated by MD simulations where dsDNA was dragged from water into
poor solvent, revealing details of the strand separation at the water/poor solvent interface. Because the
structure of DNA is of high polarity, all poor solvents show a relatively low polarity. We speculate that the
principle of spontaneous unwinding/splitting of dsDNA by providing a low-polarity (in other word, hydrophobic)
micro-environment is exploited as one of the catalysis mechanisms of helicases.