Rigid-body motions of sub-units in DNA: a correlation analysis of a 200 ps molecular dynamics simulation

A 200 ps molecular dynamics simulation of the B-form double stranded self-complementary octanucleotide d(CTGATCAG) is analyzed in terms of correlated motions using the canonical analysis approach. Each nucleotide is decomposed in three sub-units corresponding to the base, the sugar ring and the backbone respectively. The correlation between the full dynamics of two sub-units was found to decrease as their mutual distance increases. The interpretation of the full dynamics of sub-units as the superimposition of rigid-body motions (translation and orientation) and deformation shows that the main source of correlation is rigid-body motions. Correlation between sub-units deformation is weak and practically vanishes for sub-units belonging to non-adjacent nucleotides. It is also shown that the correlation is much more important for sub-units of the same strand than of opposite strands. We conclude that the internal dynamics of the octanucleotide may be well described by rigid-body motions, the sub-units deformation having only local influence whereas sub-units translation and rotation have repercussion to long distances. The results presented in this study suggest how the number of degrees of freedom may be reduced for simulating long-time dynamics of oligonucleotides.