Studies on the dynamics of DNA melting
In this study the self-consistent phonon theory is applied to the understanding of DNA melting from a microscopic point of view. Studies of the dynamics of hydrogen bond motion for a model of replicating fork at room temperature are given. The anharmonic effect increases the hydrogen bond fluctuation by more than a factor of 2 over the harmonic result in some frequency regions. The frequency dependence of the h-bond motion suggests spectral features that could be regarded as a signature for the existence of forks in DNA samples. The effect of an open loop of various sizes on the thermal stability of the adjoining intact base pairs in a duplex DNA chain is studied. For a Y-shaped fork configuration the thermal fluctuation at the fork is so enhanced that the life time of the adjoining base pair is much smaller than the 1 millisecond time scale associated with helicase separation of a base pair. The analysis indicates the significance of thermal fluctuational base pair opening in facilitating the enzyme unwinding process during chain elongation of a replicating DNA. It is likely that the thermal fluctuational opening of the base pair at the junction of a replicating fork is fast enough so that a DNA unwinding enzyme can encounter an unstacked base pair with reasonable probability. The algorithm of calculating base pair opening probability is applied to a localized structure, the replicating fork. The addition of two hot phonons to some local modes can lead to the separation of the last closed base pair. The contribution of various vibrational modes to the melting of poly(dG)[center dot]poly(dC) is studied. The principal contribution comes from the H-bond breathing modes that have been observed in Raman scattering and that have been associated with helix melting. The softening of these modes on approach to melting is in agreement with the observed behavior. The contribution to melting from base rotation modes that are important in melting is also discussed.
- Research Organization:
- Purdue Univ., Lafayette, IN (United States)
- OSTI ID:
- 7296673
- Resource Relation:
- Other Information: Thesis (Ph.D.)
- Country of Publication:
- United States
- Language:
- English
Similar Records
The E1 proteins
Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects