Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.

Abstract

The results are presented of molecular dynamics simulations on d(C-G-C-G-A).cntdot.d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the 2 simulations are similar, but the simulation with counterions does give an average helix repeat, tilt and twist in better agreement with those found in the X-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2'' endo to C3'' endo carbon conformations in the sugar ring are found. The H bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.