The dynamics of DNA--beyond the isolated double helix
Abstract
Lattice dynamics calculations of vibrational modes of DNA, specifically of A poly(dG)$\cdot$poly(dC) and B poly(dA)$\cdot$poly(dT), are performed to include more details of the medium surrounding the double helix atoms. These modes are then used to understand new experimental data for absorption of radiation in the far infrared region. The vibrational mode calculations are based on work by other investigators in which the effects of the DNA neighbors are accounted for in a dielectric model. In this case we refer to the DNA as isolated. We present four calculations of vibrational modes in which the listed near neighbors to DNA atoms are treated as atoms or ions of the lattice: they are (1) water molecules, (2) counterions, (3) a combination of water molecules and ions, and (4) a neighboring double helix. This more detailed calculation is an initial step in the process of including all of the near neighbors; thus, only a few of the near neighbors are added. For this reason, we continue to use the dielectric model which is fitted to neutron scattering data in the 10-30 cm$\sp{-1}$ range over several points in the Brillouin zone. We find that at this early stage, most of the effects are seen in the modes which have high concentrations of potential and kinetic energy in the DNA atoms closest to the near neighbors we have added. The experimental far infrared absorption data is for B poly(dA)$\cdot$poly(dT). Thus, for A poly(dG)$\cdot$poly(dC) we calculate vibrational modes only for the addition of water molecules. In calculating the absorption for isolated B poly(dA)$\cdot$poly(dT), we do not see one of the peaks given by experiment. After using the modes from the water and ion calculations, we develop a primitive model of interhelical coupling which does give a peak near 60 cm$\sp{-1}$. We thus suggest that this peak is due to the coupling between two double helices in the experimental sample.
Degree
Ph.D.
Advisors
Prohofsky, Purdue University.
Subject Area
Condensation
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