DNA displays a richness of biologically relevant
supramolecular structures, which depend on both sequence and ambient. The effect of dragging
dsDNA from water into poor solvent on the double-stranded structure is still
unclear because of condensation. Here
we employ 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 is 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 relatively low polarity. We
speculate that the principle of spontaneous unwinding/splitting of dsDNA by providing a low-polar (in other
word, hydrophobic) micro-environment is exploited as one of the catalysis
mechanisms of helicase.
