Effect of Pressure on the Conformational Landscape of a Large Loop DNA Hairpin in the Presence of Salts and Osmolytes

Abstract

The effect of pressure on the conformational landscape of a DNA hairpin has been investigated in the absence and presence of salts and osmolytes using both ensemble and single-molecule Förster resonance energy transfer (FRET) techniques.1 We use monovalent (K+), divalent (Mg2+) and trivalent (Co3+) salts and urea as well as TMAO as osmolytes. Unlike the canonical DNA duplex structures of similar melting points, this large loop DNA hairpin is rather sensitive to pressure.2 The transition volume upon unfolding is found to be −17 cm3 mol−1 in neat buffer solution. We found that the stabilizing effect of salt follows the order Co3+ > Mg2+ > K+. Above 1 mM Mg2+ and 0.3 mM Co3+, pressure has a negligible effect on the conformation of the DNA hairpin, which is due to the compensation of the negative charge density of the phosphate backbone, favoring the formation of loops by base pairing of complementary sequences, and thus the closed conformation. The compatible osmolyte TMAO also stabilizes the closed conformation even at high pressures and temperatures, while urea destabilizes the closed conformation synergistically with pressure and temperature. Intermediate states are populated by urea and high temperatures, indicating that the conformational landscape of the DNA hairpin is in fact a rugged one. The results obtained are interpreted in terms of preferential hydration and interaction effects of the cations and osmolytes.