Motion of groups of atoms in DNA studied by molecular dynamics simulation

Abstract

The analysis of Molecular Dynamics simulations of two double stranded oligonucleotides is presented in terms of motions of quasi rigid subunits. First, a strategy is presented for grouping atoms submitted to concerted internal motions. The method is based on the analysis of the interatomic distance RMS matrix. It is found that each nucleotide can reasonably be decomposed into 3 or 4 rigid groups of atoms depending on the tolerance of the definition of a rigid body. In the second part, the different kinds of motions of the subunits (deformation, translation and rotation) are studied in terms of correlation using the canonical correlation analysis of data. It is shown that the residual deformation of any subunit does not influence the translational and rotational motions of the others, except perhaps for long time dynamics.