Studies on the melting of simple DNA polymers

Kailasnath Manohar Awati, Purdue University

Abstract

The modified self-consistent phonon approximation (MSPA) has been fairly successful in predicting the melting temperatures of simple DNA polymers. In the first part of this thesis we analyze how the method works, based on free energy calculations. The analysis is very much like the Landau analysis of displacive phase transitions. We also discuss the meaning of a soft mode form of melting. There are several reasons to expect that poly(dA) $\cdot$ poly(dT) would melt at a lower temperature than poly(dAT) $\cdot$ poly(dAT). The opposite is both observed and is also the result of an MSPA calculation. The second part of this thesis explores the reason for the inversion in melting behavior that is predicted by MSPA. Vibrational states tend to accumulate in smaller frequency regions in poly(dAT) $\cdot$ poly(dAT). This seems to be the dynamical reason for its lower melting temperature. One effect of thermal fluctuations in a DNA molecule is to reduce the hydrogen bond force constants in the vicinity of the fluctuation. In the third part of this thesis we study this effect of thermal fluctuations on the vibrational spectra of poly(dG) $\cdot$ poly(dC) and poly(dA) $\cdot$ poly(dT). We assume the fluctuations create a defect (decrease in h-bond force constants) that is localized to a single base pair. In both polymers the presence of such a defect induces prominent defect modes in the frequency region between 60 and 72 $cm\sp{-1}$. The mode found in poly(dG) $\cdot$ poly(dC) is quasi-local (in-band) whereas the mode found in poly(dA) $\cdot$ poly(dT) is local (lies in the band gap). Our calculations indicate that it is easier to create the defect mode in poly(dA) $\cdot$ poly(dT) than in poly(dG) $\cdot$ poly(dC). The local mode in poly(dA) $\cdot$ poly(dT) is at a frequency where infrared absorption occurs.

Degree

Ph.D.

Advisors

Prohofsky, Purdue University.

Subject Area

Biophysics

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