Molecular dynamics simulations of d(C-G-C-G-A)·d(T-C-G-C-G) with and without 'hydrated' counterions

Abstract

We present the results of molecular dynamics simulations on d(C-G-C-G-A)·d(T-C-G-C-G) with fully charged phosphates with and without inclusions of counterions. The average structures found in the two 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 hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.