LATTICE DYNAMICS OF DNA

K. V DEVI PRASAD, Purdue University

Abstract

We seek to understand the dynamical behaviour of the biologically important macromolecule using the techniques of Solid State Physics--namely lattice dynamics. We develop a modified form of setting up the dynamical matrix for the system in terms of the Mass Weighted Cartesian Coordinates. We then develop a new long range interaction potential that in addition with the valence force field produces a good fit to the observed low frequency phonon spectrum of double helical DNA. We use the eigenvectors obtained to assign the character to some of the modes. We then use the long range potential to calculate the elastic constants of the DNA. We show that these are in agreement with relevant experimental data. We obtain the high frequency spectrum of the left handed or Z form of DNA from the dynamical matrix set up. We use the eigenvectors to assign the characteristics of the modes above 400 wave numbers. We then develop a soft mode theory of transition between different conformations. We show that the soft mode theory is applicable to the transition. We also show the mode that we identify as the soft mode based on an analysis of the eigenvectors is the same as the mode that is observed to soten as the transition takes place. By projecting out the force constants necessary to drive this mode soft we are able to predict what changes are necessary in the force constants to induce the phase transition. We show that our findings are in line with recent experimental studies.

Degree

Ph.D.

Subject Area

Biophysics

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