Atomistic model of DNA: Phonons and base-pair opening

A fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, $\sim 12.5\mathrm{meV}$, a continuous band of modes with strong base-pair opening character is found up to $40\mathrm{meV}$, which coincides with the typical denaturation temperature of DNA.

Figure 1

Calculated dispersion curves of the 20 lowest modes (a) and the apparent dispersion (b) obtained by fitting the spectral intensity. X-ray data are taken from [8].

Figure 2

Projection analysis of eigenvectors as a function of frequency.

Figure 3

(Color online) Selected eigenvectors, in a bead representation, showing strong radial (top left), axial (top right), and breathing (bottom) character. The mode frequencies are, respectively, 1.92, 1.71, and $9.51\mathrm{meV}$.

Figure 4

Breathinglike character of modes as a function of energy using a base molecule as a bead and a whole nucleotide as a bead, respectively.