To decide whether counterions can affect the rate of charge recombination in DNA hairpins, the influence of the salt concentration on the free energy of this process was studied computationally using molecular dynamics simulations. The calculations were performed using the implicit treatment of the surroundings (the MM-PBSA and MM-GBSA techniques) and the explicit description of counterions and water molecules (thermodynamic integration). The data obtained with these distinct approaches were found to be in good agreement. The effect of counterions on the free energy of the charge recombination process was found to be small. For the hairpins with six A/T base pairs between the donor and acceptor chromophores, the difference in the value of the free energy does not exceed 0.5 kcal/mol when the environment changes from pure water to the 0.1 M NaCl solution typical for kinetic measurements of charge recombination in DNA hairpins. Even a smaller salt effect has numerically been obtained for a shorter hairpin containing three A/T pairs. These results suggest that under typical experimental conditions, the counterions cannot control the rate of charge recombination. For a highly concentrated salt solution (1 M NaCl), the influence of counterions on the energetics of the process becomes stronger. Since in this case the free energy for charge recombination exhibits a more substantial but still kinetically insignificant increase, the calculated rate of the process only slightly decreases with the salt concentration.
ASJC Scopus subject areas
- Electronic, Optical and Magnetic Materials
- Physical and Theoretical Chemistry
- Surfaces, Coatings and Films