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Using RNA backbone torsions to study RNA structure
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Text
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Using RNA backbone torsions to study RNA structure
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ETD_2305
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http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000052134
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eng
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theses
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Microbiology and Molecular Genetics
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Topic
RNA
Subject
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Topic
Nucleotide sequence
Abstract
Ribonucleic Acid (RNA) is an important cellular macromolecule vital to most if not all life on Earth. RNA has many different roles in the cell, most notably as the intermediary molecule that transfers genetic information from DNA to protein in translation. Recently, additional functions of RNA have been elucidated more clearly, such as catalyzing chemical reactions and regulating gene expression. These exciting new findings have shined a scientific spotlight on the field of RNA structure in order to better understand how the once mundane polynucleotide acts in such myriad ways.
An important factor in RNA’s versatile nature is the inherent variation in its chemical structure. The hydroxyl group present on the ribose sugar of a ribonucleic acid makes the corresponding polynucleotide capable of chemical reaction, with itself or with other molecules in the cell. This hyper-reactivity allows RNA to form substantially unique structures, from the hammerhead ribozyme's helical shape from which it takes its name, to the L-shaped conformation common to all transfer RNAs. The problem at hand is thus to study RNA structure and determine if any new patterns can be discovered.
The work presented here centered on a collaborative effort to define a set of conformations common to two-nucleotide long sequences of RNA found in structures from the Protein Data Bank (PDB). This work contributed by clustering RNA di-nucleotides by their torsion angle space using a Fast Fourier averaging technique proven to be effective in clustering nucleotide structure. Each group in the collaboration used different methodologies to analyze the same RNA structural data, and yet found similar results. The collaboration ultimately produced a set of 46 consensus conformations defined by the seven dihedral angles of the sugar-to-sugar unit in a di-nucleotide RNA sequence.
To utilize this new set of RNA di-nucleotide conformations, a software tool was designed and developed to automatically assign the conformation nomenclature to input RNA structure. The program was successfully tested on the pilot study data. A test study was performed on a unique set of RNA structures. The results of this study demonstrated that the consensus conformation set can in fact be used to classify RNA structure.
An important factor in RNA’s versatile nature is the inherent variation in its chemical structure. The hydroxyl group present on the ribose sugar of a ribonucleic acid makes the corresponding polynucleotide capable of chemical reaction, with itself or with other molecules in the cell. This hyper-reactivity allows RNA to form substantially unique structures, from the hammerhead ribozyme's helical shape from which it takes its name, to the L-shaped conformation common to all transfer RNAs. The problem at hand is thus to study RNA structure and determine if any new patterns can be discovered.
The work presented here centered on a collaborative effort to define a set of conformations common to two-nucleotide long sequences of RNA found in structures from the Protein Data Bank (PDB). This work contributed by clustering RNA di-nucleotides by their torsion angle space using a Fast Fourier averaging technique proven to be effective in clustering nucleotide structure. Each group in the collaboration used different methodologies to analyze the same RNA structural data, and yet found similar results. The collaboration ultimately produced a set of 46 consensus conformations defined by the seven dihedral angles of the sugar-to-sugar unit in a di-nucleotide RNA sequence.
To utilize this new set of RNA di-nucleotide conformations, a software tool was designed and developed to automatically assign the conformation nomenclature to input RNA structure. The program was successfully tested on the pilot study data. A test study was performed on a unique set of RNA structures. The results of this study demonstrated that the consensus conformation set can in fact be used to classify RNA structure.
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electronic resource
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xii, 70 p. : ill.
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M.S.
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Includes bibliographical references (p. 63-70)
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by David Ian Micallef
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Micallef
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David Ian
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1979-
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David Ian Micallef
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Helen
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Helen Berman
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Levy
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Ronald
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Ronald Levy
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Olson
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Wilma
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Wilma Olson
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Rutgers University
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Graduate School - New Brunswick
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2010
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2010-01
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xx
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Rutgers University Electronic Theses and Dissertations
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ETD
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Graduate School - New Brunswick Electronic Theses and Dissertations
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doi:10.7282/T34F1QV3
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ETD graduate
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The author owns the copyright to this work.
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Copyright protected
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Open
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Permission or license
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Micallef
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David
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2009-12-15 15:33:13
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David Micallef
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Rutgers University. Graduate School - New Brunswick
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Author Agreement License
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I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
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