Phonon theory of DNA processes--a study of excitations and melting

Vinayakumar V Prabhu, Purdue University

Abstract

The DNA molecule is considered as an infinite one dimensional lattice. Its processes are comprehended in terms of phonons traversing the polymer. We commence our understanding of the essential dynamics of the molecule by deriving dispersion relations, i.e. relations between wavelength and frequency of waves in the lattice. The DNA molecule contains information essential for life processes in the sequence of bases in its strands. When this information is sought to be communicated to the cell a partial strand separation is a prerequisite to revealing the code in the base sequence. Replication of DNA requires total strand separation. We have conceived of such strand separation as a melting of hydrogen bonds connecting the two strands. We model the lattice in terms of harmonic force constants and examine the stretching of the hydrogen bonds. Then, we selectively introduce anharmonicity in the hydrogen bond force constants as the temperature increases. This is done through a mean field self consistent phonon approach. The breakdown of self consistency is interpreted as a breakdown of the effective hydrogen bond force constants and hence as melting. To study the relative influences of the A-T and G-C base pairs, we have examined 5 copolymers whose unit cells are GCCG, ACGT, AGCT, ATAT in the B conformation and GCGC in the Z conformation. (Here GCGC implies that the unit cell is composed of two base pairs with a C-G pair following a G-C pair). We find good correlation with experimental results on DNA excitations. By our calculations the mean field melting temperatures in K are 385, 366, 357, 325 for the B-DNA copolymers. Our calculations reveal specific bonds in the unit cell that initiate the melting. This is one step in understanding the significant mechanisms of transcription and replication in the DNA molecule.

Degree

Ph.D.

Advisors

Prohofsky, Purdue University.

Subject Area

Condensation

COinS