Normal mode analysis of a double-stranded DNA dodecamer d(CGCGAATTCGCG)

The normal mode analysis in dihedral angle space is carried out on a famous double-stranded DNA dodecamer d(CGCGAATTCGCG) to reveal the dynamical characteristics and internal motion of this molecule. We have observed the coupled motion of sugar and base. We have also noted the dependence of internal motion in the dodecamer on location of the nucleotide relative to the helical ends, and the dependence of atomic fluctuations on distance from the helix axis. The similarity of atomic fluctuations between two strands suggests the presence of a twofold pseudosymmetry axis with its origin located at the center of the molecule. Our results show that the atomic fluctuations of duplex DNA are mainly determined by a small number of low-frequency normal modes, the normal modes with frequencies below 30 cm−1 make major contributions to the site-dependence of atomic fluctuations.