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The analysis and prediction of DNA structure

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dc.contributor.advisor Ho, P. Shing
dc.creator Basham, Beth E.
dc.date.accessioned 2012-09-27T18:34:27Z
dc.date.available 2012-09-27T18:34:27Z
dc.date.copyright 1998-03-11
dc.date.issued 1998-03-11
dc.identifier.uri http://hdl.handle.net/1957/33950
dc.description Graduation date: 1998 en_US
dc.description.abstract As genome sequencing projects begin to come to completion, the challenge becomes one of determining how to understand the information contained within the DNA. DNA is a polymorphic macromolecule; the A- B- and Z-DNA conformations have been observed by a variety of physical techniques. The magnitude of the energetic differences between these conformations suggests that these conformations may be important biologically and thus relevant in the analysis of genomes. A computer program, NASTE, was developed to evaluate the helical parameters of the set of Z-DNA crystal structures in order to determine the true conformation of Z-DNA and to understand the effects of various factors on the observed structure and stability. A thermodynamic method, elucidated in part with a genetic algorithm, was developed to predict the sequence-dependent propensity of DNA sequences for A- versus B-DNA in both the crystal and in natural DNA. Predictions from this method were tested by studying the conformation of short oligonucleotides using circular dichroism spectroscopy. Finally, the thermodynamic method was applied in an algorithm, AHUNT, to identify regions in genomic DNA with a high propensity to form A-DNA. Significant amounts of A-DNA were identified in eukaryotic and archeabacterial genes. E. coli genes have less A-DNA than would be predicted from their (G+C) content. These results are discussed with respect to the intracellular environment of the genomes. en_US
dc.language.iso en_US en_US
dc.subject.lcsh DNA -- Analysis en_US
dc.subject.lcsh DNA -- Structure en_US
dc.title The analysis and prediction of DNA structure en_US
dc.type Thesis/Dissertation en_US
dc.degree.name Doctor of Philosophy (Ph. D.) in Biochemistry and Biophysics en_US
dc.degree.level Doctoral en_US
dc.degree.discipline Science en_US
dc.degree.grantor Oregon State University en_US
dc.description.digitization File scanned at 300 ppi (Monochrome, 8-bit Grayscale) using ScandAll PRO 1.8.1 on a Fi-6770A in PDF format. CVista PdfCompressor 4.0 was used for pdf compression and textual OCR. en_US
dc.description.peerreview no en_us

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