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The effect of cytosine methylation on DNA structure

DNA methylation is common in prokaryotes and eukaryotes and has been
implicated in various biological roles including gene silencing, X-chromosome
inactivation, and genomic imprinting. 5-methylcytosine the "fifth base" of the
genetic code comprises 1-3% of the human genome and is primarily found on
cytosines within the context of the CpG sequence. Although progress has been
made in understanding the biological roles of 5-methylcytosine, we are only
beginning to uncover how it changes the local structure and global conformation of
DNA. This thesis deals with the local perturbations in structure and hydration and
the global conformational changes induced by the presence of 5-methylcytosine in
DNA as determined by single crystal x-ray diffraction.
5-methylcytosine induces a novel conformation in the structure of duplex
DNA. This conformation has characteristics of both the A-DNA and B-DNA
conformations as well as some unique defining characteristics. This distinct duplex
provides a structural rationale for the increased rate of deamination in 5-methylcytosine relative to cytosine. In addition to this novel conformation, 5-methylcytosine stabilizes intermediates within the B-DNA to A-DNA transition pathway, thus providing a crystallographic map of the transition from B-DNA to A-DNA.
5-methylcytosine was also used as a tool to probe the stabilizing features of
the DNA four-way junction (known as the Holliday junction). The first crystal
structures of Holliday junctions were found serendipitously while studying duplex
DNA. The DNA four-way junction formation in these crystals was thought to be
stabilized by a network of sequence dependent hydrogen bonds at the junction
crossover. In this thesis, 5-methylcytosine was used to perturb these hydrogen
bonds; however, the junction persisted, suggesting that there is flexibility in the
types of sequences that can accommodate junction formation in the crystal, as well
as, flexibility in the global structure of the junction. Overall, this work describes
the effects of 5-methylcytosine on the local and global structure and hydration of
DNA structure, as well as raising some interesting questions regarding the
biological impact of methylation induced DNA structure. / Graduation date: 2002
Date26 February 2002
CreatorsVargason, Jeffrey M.
ContributorsHo, Pui Shing
Source SetsOregon State University
Detected LanguageEnglish

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