Feb 4, 1998

Solvent influence on base stacking

Biophysical Journal
J Norberg, L Nilsson

Abstract

In this paper we present a detailed analysis of the base-stacking phenomenon in different solvents, using nanosecond molecular dynamics simulations. The investigation focuses on deoxyribo- and ribodinucleoside monophosphates in aqueous and organic solutions. Organic solvents with a low dielectric constant, such as chloroform, and solvents with intermediate dielectric constants, such as dimethyl sulfoxide and methanol, were analyzed. This was also done for water, which is highly polar and has a high dielectric constant. Structural parameters such as the sugar puckering and the base-versus-base orientations, as well as the energetics of the solute-solvent interactions, were examined in the different solvents. The obtained data demonstrate that base stacking is favored in the high dielectric aqueous solution, followed by methanol and dimethyl sulfoxide with intermediate dielectric constants, and chloroform, with a low dielectric constant.

  • References21
  • Citations28

References

  • References21
  • Citations28

Citations

Mentioned in this Paper

C1S
Thermodynamics
Molecular Dynamics
In Silico
FEN1
Dimethyl Sulfoxide
Sodium Methoxide
Surface Properties
Organic solvent product
Calorimetry

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