For about 50 years it has been known that guanine-rich sequence can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from both sequence analysis and function-specific assays. The folds are unusually stable and their formation appears to require close management to maintain cell health; regulatory failure correlates with genomic instability and a number of cancer phenotypes.
This thesis examines, by x-ray crystallography, the solvent structure of a previously reported tetramolecular RNA quadruplex, UGGGGU stabilized by Sr2+ ions. Crystal forms of the octameric assembly formed by this sequence exhibit unusually strong diffraction and anomalous signal enabling the construction of reliable models to a resolution of 0.85 Å. The solvent structure confirms hydration patterns reported for other nucleic acid helical conformations and provides support for the greater stability of RNA quadruplexes relative to DNA. Novel features detected in the octameric RNA assembly include a new crystal form and evidence of multiple conformations, among which one leading to the formation of a well-hydrated internal cavity.
Though solvent is generally acknowledged to play a fundamental role in nucleic acid structure, its characterization from diffraction data remains challenging. To assist with this task, the thesis investigates two novel additions to the crystallographic methods arsenal. The first is segmentation of electron density maps into Morse-Smale basins characterized by uniform gradient flow. The second is the use of level set Fast Marching methods to compute the full distance field defined by the molecular surface. Both techniques show promise, though additional work will be required to yield effective tools. Gradient-flow segmentation provides an unambiguous way to gather all map density associated with a modeled atom and enables the calculation of novel volumetric properties including total basin density. Distance field calculation provides a unified framework for combining molecular surface calculation with surface-related queries including pocket and cavity detection and solvent travel depth.
|Advisor:||Scott, William G.|
|Commitee:||Karplus, Kevin, Switkes, Eugene|
|School:||University of California, Santa Cruz|
|Department:||Biomolecular Engineering and Bioinformatics|
|School Location:||United States -- California|
|Source:||DAI-B 74/01(E), Dissertation Abstracts International|
|Subjects:||Molecular biology, Biochemistry, Biophysics|
|Keywords:||Crystallography, High-resolution, RNA quadruplex, Solvents|
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