Properties and conformation of P-form DNA Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/rv042w827

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  • Work is presented which explores the properties and nature of the P-form of DNA. Initially the P-form represented an unknown state of DNA which occurred when this molecule was in a solvent of 47.5% methanol, 5% water, and 47.5% ethanol, and which showed properties of both native and denatured conformations. In the first part of this thesis data are shown that (1) demonstrate that the Pform also exists as an irreversible function of temperature in solvents containing only 5% water but ranging from 95% to 47.5% methanol and 47.5% to 0% ethanol, (2) extend the circular dichroism spectrum of the P-form into the far UV where its low intensity indicates a lack of base stacking, and (3) demonstrate that the P-form in these solvents has an unusual and unexpectedly high heat stability. These data are interpreted to show that the P-form must be caused by a structural change within the DNA molecule, and several structural models are proposed that may account for the data acquired. The latter part of this work presents experiments which prove that the P-form structure is a combination of collapsed tertiary and denatured secondary structures. The presence of a collapsed tertiary structure is first indicated in viscosity data and is then demonstrated by the actual visualization of the condensed state with electron microscopy. The denatured state of the molecule is first hinted at in a delayed 10.2 to P-form transition in covalently closed circular DNA, and then proved when infrared spectroscopy shows that there is no hydrogen bonding in the P-form structure. This condensed-denatured structure for the P-form fully explains all of the seemingly contradictory properties of this state.
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