TY - JOUR
AU - Hsuan-Lei Sung
AU - David Nesbitt
AB - Pressure may perturb biomolecular function by altering equilibrium structures and folding dynamics. Its influences are particularly important to deep sea organisms, as maximum pressures reach up to ≈ 1100 bar at the bottom of the ocean as a result of the rapid increase in hydraulic pressure (1 bar every 10 meters) under water. In this work, DNA hybridization kinetics has been studied at the single molecule level under external pressure control (Pmax ≈ 1500 bar), realized by incorporating a mechanical hydraulic capillary sample cell into a confocal fluorescence microscope. We find that the DNA hairpin construct unfolds (“denatures”) with increasing pressure by simultaneously decelerating and accelerating the unimolecular rate constants for folding and unfolding, respectively. The single molecule kinetics is then investigated via pressure dependent van’t Hoff analysis to infer changes in the thermodynamic free volume, which unambiguously reveals that the effective DNA plus solvent volume increases (V0 > 0) along the folding coordinate. Cation effects on the pressure dependent kinetics are also explored as a function of monovalent [Na+]. In addition to stabilizing the overall DNA secondary structure, sodium ions at low concentrations are also found to weaken any pressure dependence for the folding kinetics, but with these effects quickly saturating at physiologically relevant levels of [Na+]. In particular, the activation volumes for the DNA dehybridization (ΔV‡unfold) are significantly reduced with increasing [Na+], suggesting that sodium cations help DNA adopt a more fold-like transition state configuration.
BT - Physical Chemistry Chemical Physics
DA - 2020-10
DO - 10.1039/D0CP04035E
IS - 41
N2 - Pressure may perturb biomolecular function by altering equilibrium structures and folding dynamics. Its influences are particularly important to deep sea organisms, as maximum pressures reach up to ≈ 1100 bar at the bottom of the ocean as a result of the rapid increase in hydraulic pressure (1 bar every 10 meters) under water. In this work, DNA hybridization kinetics has been studied at the single molecule level under external pressure control (Pmax ≈ 1500 bar), realized by incorporating a mechanical hydraulic capillary sample cell into a confocal fluorescence microscope. We find that the DNA hairpin construct unfolds (“denatures”) with increasing pressure by simultaneously decelerating and accelerating the unimolecular rate constants for folding and unfolding, respectively. The single molecule kinetics is then investigated via pressure dependent van’t Hoff analysis to infer changes in the thermodynamic free volume, which unambiguously reveals that the effective DNA plus solvent volume increases (V0 > 0) along the folding coordinate. Cation effects on the pressure dependent kinetics are also explored as a function of monovalent [Na+]. In addition to stabilizing the overall DNA secondary structure, sodium ions at low concentrations are also found to weaken any pressure dependence for the folding kinetics, but with these effects quickly saturating at physiologically relevant levels of [Na+]. In particular, the activation volumes for the DNA dehybridization (ΔV‡unfold) are significantly reduced with increasing [Na+], suggesting that sodium cations help DNA adopt a more fold-like transition state configuration.
PB - "The Royal Society of Chemistry"
PY - 2020
SP - 23491
EP - 23501
T2 - Physical Chemistry Chemical Physics
TI - Single-Molecule Kinetic Studies of DNA Hybridization Under Extreme Pressures
UR - http://dx.doi.org/10.1039/D0CP04035E
VL - 22
ER -