Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations

Although the thermodynamic stability of ordered DNA is known to be affected by interactions with cations and water molecules, there is scarce quantitative information about the behavior of DNA under conditions of molecular crowding as found inside the cell. In this study, we measured the thermal stability of DNA base pairs under conditions of molecular crowding caused by polyethylene glycol (PEG) and at different concentrations of NaCl. Even though PEG 200 and 8000 (average molecular weights of 200 and 8000, respectively) decreased the stability of DNA base pairs at high NaCl concentrations, PEG 8000 substantially increased the stability at low NaCl concentrations. Quantitative analyses of the thermodynamic parameters made it possible to determine the numbers of water molecules (−Δnw) and sodium ions (−ΔnNa+) bound to the hairpin DNA. These measurements showed that PEG decreased the −ΔnNa+ value without changing the −Δnw value, suggesting that PEG buffers sodium ion binding but may not affect the hydration status of the nucleotide or sodium ion. These results should help clarify the effects of molecular crowding on DNA stability and function and provide quantitative information about the effects of molecular crowding in cells and on chips and nanoparticles.