TCB Publications - Paper Request

Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub. Double stranded DNA dissociates into single strands when dragged into a poor solvent. Journal of the American Chemical Society, 129:14710-14716, 2007.

CUI2007 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 doublestranded 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 relative 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.

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