Molecular dynamics simulations of DNA oligomers under various electrostatic parameters

Abstract

The modelling program AMBER 3.0 has been used to generate molecular dynamics trajectories of d(A-T) and dA-dT oligomers. The simulations were done without explicit solvent molecules but with two different dielectric functions (e(r) = 4r and a sigmoidal distance-dependent dielectric function e(r) = e cal ) as well as with and without derivation of the additional distance-dependence introduced. Best comparisons between experimental (Raman, NMR, X-ray data) and calculated results are obtained with the c dielectric function with derivation of the distance-dependence of the dielectric function. Thus, the pseudorotation phases of the adenine residues are systematically higher (around C 2’ -endo) than those of the thymine residues (close to O 4’ -endo). Also, depending on the dielectric function, the lifetimes of the Watson-Crick H-bonds are 10 to 50 times longer than those of the three-centered H-bonds in the major groove of dA-dT.