Graduation Year

2013

Document Type

Open Access Senior Thesis

Degree Name

Bachelor of Arts

Department

W.M. Keck Science Department

Second Department

Biochemistry

Reader 1

Mary Hatcher-Skeers

Reader 2

Len Mueller

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© 2012 Caitlin A. Edmunds

Abstract

The interaction of deoxyribonucleic acid (DNA) and cellular proteins is absolutely central to any biological understanding of DNA replication, transcription, and even gene regulation. Because an incumbent protein latches not onto the four bases but onto the backbone phosphate groups of the nucleic acid, backbone dynamics directly pertain to an understanding of basic cell processes. Studies have unambiguously proven that DNA exists in a balance of two conformations, BI and BII, defined by the difference in their backbone torsion angles. A given DNA sequence expresses a preference for either BI or BII, though both exist in most samples (and are presented as a ratio). Factors affecting that ratio include flanking sequence and methylation. When a DNA sample is methylated, which occurs at a cytosine, backbone dynamics at that site and perhaps even its neighbors are theoretically quenched due to the steric strain of a large attached group. DNA methylation is implicated in cancer diagnosis by new studies focusing on hypermethylation in CpG islands,

This thesis uses solid-state deuterium NMR to study the backbone dynamics of the Dickerson dodecamer, [d(CGCGAATTCGCG)]2, which was the first synthetic BII conformer successfully crystallized (allowing for analysis in the solid state) and which contains the EcoRI binding site, GAATTC. This molecule is a good model system because a massive amount of information has been gathered on it not only using NMR, both high-resolution and solid-state, but also using x-ray diffraction, electron paramagnetic resonance, and all-atom molecular dynamics simulation. This thesis research shows the quenching of backbone dynamics due to C9 methylation.

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