Molecular Dynamics Studies of the Conformational Preferences of a DNA Double Helix in Water and an Ethanol/Water Mixture: Theoretical Considerations of the A ⇔ B Transition

Abstract

A series of molecular dynamics (MD) computer simulations were carried out to explore the conformational preferences of a dynamic model of the sodium salt of the DNA duplex d(CGCGAATTCGCG) in water and in a mixed solvent comprised of 85% (v/v) ethanol/water. This sequence is observed to assume a B-form structure in the solid state and in aqueous solution and is expected to assume an A-form structure in the mixed solvent environment. The MD simulations are based on the empirical force field proposed recently by Cornell et al.1 and carried out with long-range interactions treated via the particle mesh Ewald method using the AMBER 4.1 modeling package.2-4 This study builds on the results of a previous 5 ns MD simulation on d(CGCGAATTCGCG) in water,5 now extended to 13 ns, which resulted in a well-stabilized B-form dynamical structure. Three additional simulations are reported: one simulation starts from the A-form in water, the second starts from the A-form in 85% (v/v) ethanol/water, the last starts from th...