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Studies on the dynamics of DNA melting

Purdue University
Publication Date
  • Physics
  • Condensed Matter|Biophysics
  • General
  • Biology
  • Computer Science


In this study the self-consistent phonon theory is applied to the understanding of DNA melting from a microscopic point of view. Chapters 1 and 2 together present an overview of the theory. In Chapter 3 studies of the dynamics of hydrogen bond motion for a model of replicating fork at room temperature is given. It is found that the anharmonic effect increases the hydrogen bond fluctuation by more than a factor of 2 over the harmonic result in some frequence 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 in chapter 4 and 5. It is found that 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. Our 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 most 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. This conclusion can explain several experimental observations regarding the temporal relationship between ATP hydrolysis by accessory proteins and primer elongation by a holoenzyme complex in ssDNA.^ In chapter 6 the algorithm of calculating base pair opening probability is applied to a localized structure, the replicating fork. It is found that the addition of two hot phonons to some local modes can lead to the separation of the last closed base pair.^ In chapter 7 the contribution of various vibrational modes to the melting of poly(dG)$\cdot$poly(dC) is studied. It is found that 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. It is shown that 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 have suggested by others that are important in melting is also discussed. ^

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