Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 49 for “"RNA structures"”.
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Using Domination to Analyze RNA Structures.
<p>Understanding RNA molecules is important to genomics research. Recently researchers at the Courant Institute of Mathematical Sciences used graph theory to model RNA molecules and provided a database of trees representing possible secondary RNA structures. In this thesis we use domination …
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Analytic Combinatorics Applied to RNA Structures
… it has been shown that the folding pattern of an RNA molecule plays an important role in its function, likened to a lock and key system. γ-structures are a subset of RNA pseudoknot structures filtered by topological genus that lend themselves nicely to combinatorial analysis. Namely, the …
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Targeting RNA Structures with Multivalent Branched Peptide Libraries
RNA is essential for the transfer of genetic information, as the central dogma of biology dictates. The role of RNA, however, is not limited to serving as an information shuttle between DNA and fully functional protein. Indeed, RNA has experienced a surge of interest in the field of chemical …
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Computational Techniques Applied to RNA Structures and Bacterial Genomes
… for studies associated with atomic resolution structures and/or NextGen sequencing. In this dissertation, three separate studies are described in which modern computational methodologies play a key role. The first case is a model system that seeks to understand how complexity might arise in a …
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The role of RNA structures in the evolution of respiratory RNA virus genomes.
RNA secondary structures in RNA viral genomes play important roles in a range of functions, including packaging, protection from cellular nucleases, and regulating viral replication. Furthermore, RNA structures have been shown to be immunostimulatory. In the case of Influenza A virus (IAV), during …
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A new approach to feature extraction for RNA structure comparision
In recent years, RNA structural comparison becomes a crucial problem in bioinformatics research. Generally, it is a popular approach for representing the RNA secondary structures with arc-annotation sets. Several methods can be used to compare two RNA structures, such as tree edit distance, longest …
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Development of pattern recognition technique for classification of RNA secondary structures by small molecules
<p>Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. In this dissertation, I will discuss the development of a pattern recognition technique which utilizes differential binding …
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Improved Algorithms for Alignment between RNA Tertiary Structures
RNA is an important molecule which performs a wide range of functions in biological systems. The comparison between RNA secondary and tertiary structures has received much attention recently. It is a well known fact that structural features of RNAs are among the most significant factors in the …
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The Multifunctional Capsid Gene of Hepatitis C Virus
… conserved and this has led to predictions of RNA secondary structure and an overlapping, alternative reading frame (ARF). We investigated a role of the ARF in HCV infection, by introducing four stop codons into the ARF of a genotype 1a H77 molecular clone. These changes did not alter the …
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Physics-based predictions of RNA loop stability and structures
… OF MISSOURI-COLUMBIA AT AUTHOR'S REQUEST.] RNA (ribonucleic acid) molecules play a variety of crucial roles in cellular functions at the level of transcription, translation and gene regulation. RNA functions are tied to structures. In parallel to the experimental determination of RNA …
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DOCKGROUND Protein Docking Benchmark Sets and Assessment Resource
… few experimentally determined protein-protein structures available. Protein-RNA structures are especially difficult to solve experimentally because of the significant flexibility of RNA. Thus, compared to the protein-protein complexes there are even fewer structures of protein-RNA complexes …
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Investigating and Reprogramming RNA Folding with Molecular Probes
Ribonucleic acid (RNA) performs versatile, essential functions in all known organisms and viruses. These functions require the RNA to fold into specific secondary and tertiary structures, and in many cases to switch among multiple structural states. Predicting and experimentally determining RNA …
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Graphical methods in RNA structure matching
… almost every base can be found in an RNA transcript. This is a surprising observation since most of the genome does not encode proteins. This RNA must serve an important regulatory function – important because producing non-coding RNA is an energy intensive process, and in the absence …
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Nucleobase, Nucleoside, And Neighboring Nucleotides: Intrinsic Preferences For Tet Enzyme-Mediated Oxidation Of 5-Methylcytosine
… with regards to different nucleic acid structures, sequence contexts, and extent to which TET mediates oxmCs in clustered proximity to one another. Thus, in this thesis, I present our efforts to determine intrinsic substrate preferences of TET enzymes, and in doing so expand upon our …
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FUNCTIONAL ANALYSIS OF THE UPSTREAM PSEUDOKNOT DOMAIN AND ITS SUBSTITUTION WITH A POLY(A) TRACT IN TOBACCO MOSAIC VIRUS (TMV)
… DEEP SEQUENCING RESULTS SHOWED THAT SMALL RNA PROFILES DIFFERED BETWEEN TMV- AND TMV-43A-INFECTED PLANTS. SEVERAL VIRAL SMALL INTERFERING RNAS DERIVED FROM TMV-UPD WERE PREDICTED TO TARGET HOST GENES. RNA STRUCTURES WERE ANALYZED USING SELECTIVE 2'-HYDROXYL ACYLATION ANALYZED BY PRIMER …
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A Predictive Model Which Uses Descriptors of RNA Secondary Structures Derived from Graph Theory.
<p>The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and …
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Translation of Partially Decayed Messenger RNAs in Yeast
… are positive-strand single-stranded RNA viruses that are known to form pseudo-knot RNA structures that halt the progression of 5’→3’ exonuclease Xrn1. We show that these viral Xrn1-resistant structures (xrRNAs) can be used to protect specific homologously-expressed messenger RNAs from …
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A study of the molecular mechanism of the attenuation response in the threonine operon of Escherichia coli by synthesis of mutant attenuators
… of the competing terminator and antiterminator RNA structures in attenuation regulation of the thr operon of Escherichia coli, nine related attenuators with altered symmetry were made. Transfersions that destroy or invert a base pair near the middle of the base paired regions of the alternative …
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The conformational landscape of RNA translational regulators and their potential as drug discovery targets
RNA is an underutilized target for drug discovery. Once thought to be a passive carrier of genetic information, RNA is now known to play a critical role in essentially all aspects of biology including signaling, gene regulation, catalysis, and retroviral infection. It is now well-established that …
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