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Showing 1 to 20 of 61 for “"Ribozyme"”.
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Dynamics of Hairpin Ribozyme
… spectroscopy to study the dynamics of hairpin ribozyme---an enzymatic RNA molecule capable of cleaving phosphodiester linkage. RNA controls key processes of gene expression. Ribozymes can catalytically edit precursor RNA message transcribed from DNA, the edited RNA then carries the genetic …
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Single molecule fluorescence and force spectroscopy of hairpin ribozyme
Submitted by Elizabeth Kent (eckent2@illinois.edu) on 2012-06-07T18:47:11Z No. of bitstreams: 1 2006_nahas.pdf: 5361832 bytes, checksum: 0d81d12a930597d8c5ce651d401a9bd7 (MD5)
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Étude du chemin réactionnel du ribozyme de l'hépatite D humaine
… d'un ARN modèle hautement structuré: le ribozyme de l'hépatite D humaine (ribozyme HDV). L'idée est que s'il est possible de comprendre dans les moindres détails une structure complexe, ces informations pourront être utilisées pour la prédiction de structures plus simples. Premièrement, …
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Kinetic barriers to folding in the Tetrahymena group I ribozyme
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1998.
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Computational studies of the self-cleavage mechanism in the glmS ribozyme
Ribozymes are catalytically functional RNA molecules. To overcome the lack of structural and chemical diversity, ribozymes employ several interesting strategies for catalysis. The glmS ribozyme regulates the level of glucosamine-6-phosphate (GlcN6P) in bacteria by catalyzing a self-cleavage …
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Nucleotide recognition and metal ion requirements of an RNA ligase ribozyme
The class I ligase, a ribozyme previously isolated from random sequence, catalyzes a reaction similar to RNA polymerization, positioning its 5'-nucleotide via a Watson-Crick base pair, forming a 3',5'-phosphodiester bond between its 5'-nucleotide and the substrate, and releasing pyrophosphate. The …
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Enhancement of anti-HIV-1 Ribozyme Activities by Rev Binding and Multimerization
<p>To effectively apply hammerhead ribozymes as therapeutic agents it is necessary to co-localize them with the desired target. Human immunodeficiency virus type1 (HIV- 1) infectivity is dependent on <em>env</em> gene expression. HIV-1 Rev protein binds to a higher ordered RNA structure within the …
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Deoxyribozyme-Mediated Synthesis of Branched Nucleic Acids and Application to Modulation of Ribozyme Catalysis
Deoxyribozymes are single-stranded DNA molecules that catalyze a variety of chemical reactions. Catalytic DNAs have not been found in nature but can be identified by in vitro selection from random sequences. In this thesis, deoxyribozymes that ligate two RNA substrates or attach DNA to RNA are …
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Computational studies of the structure, dynamics, and catalysis of the hepatitis delta virus ribozyme
Ribozymes represent a unique class of RNA that is capable of catalyzing biochemical reactions. Since their discovery three decades ago, ribozymes have been shown to be involved in numerous crucial biological processes, such as gene regulation, translation, and RNA splicing. Similar to protein …
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Studies of the Catalytic-Metal-Binding Site in the Hammerhead Ribozyme Using the Phosphorothioate Approach
… of metal ions with phosphate oxygens in the ribozyme structure. An enhancement in cleavage rate upon addition of a softer metal ion than Mg2+, such as Mn2+ is taken as evidence for coordination of the metal ion to the phosphorothioate sulfur and by analogy, an interaction of Mg 2+ with oxygen …
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Investigating and expanding the functionality of RNA catalysts: Studies of the hepatitis delta virus, the hammerhead, and the aminoacyl-tRNA synthetase-like ribozymes
<p>Ribozymes, just like protein enzymes, catalyze diverse chemical reactions. The first goal of this dissertation is to understand the mechanism of ribozyme-mediated phosphodiester cleavage reaction. Biochemical assays and X-ray crystallography were used for probing the active site of two small …
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Ice as a medium for RNA-catalysed RNA synthesis and evolution
… this could have been an RNA polymerase ribozyme capable of generating copies of itself from simple nucleotide precursors. In vitro evolution experiments have provided modern examples of such ribozymes, such as the R18 RNA polymerase ribozyme, exhibiting basic levels of this crucial …
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Searching for ribozymes with new and improved properties
… space. In Chapter 1 I investigated how readily ribozymes with new catalytic activities and folds could arise from an existing ribozyme scaffold. In vitro selection was used to isolate 23 kinase ribozymes from a pool of more than 104 variants of an aminoacylase parent ribozyme. The density of …
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Design and synthesis of probes for detection of protein-protein interaction and RNA localization
… probes were synthesized for the selection of ribozymes from a random sequence pool. Solid-phase immobilized fluorescein and fluorescein phosphates were synthesized for the indirect selection of a fluorescein phosphatase ribozyme. A corresponding thiophosphate analog was created for the in-gel …
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Engineering RNA logic with synthetic splicing ribozymes
… In this thesis, I show the utility of splicing ribozymes for the biological engineer. Ribozymes allow the engineer to manipulate existing biological systems and to program self-modifying RNA systems. In addition, splicing ribozymes are easy to engineer, malleable, modular, and scalable. I used …
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Development of Catalytic RNAs as Potential Anti-HIV-1 Agents
<p>RNA molecules with enzymatic activity (ribozymes) targeted to the genome of HIV-1 were developed and demonstrated to mediate site-specific cleavage of the HIV-1 RNA in vitro and to inhibit viral proliferation intracellularly. Two classes of ribozymes that incorporate a "hammerhead" catalytic …
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Cellular uptake and biological activity of synthetic hammerhead ribozymes
… as a causative factor of tumourigenesis. Ribozymes are a class of ribonucleic acid that possess enzymatic properties. They can inhibit gene-expression in a highly sequence specific manner by catalysing the trans-cleavage of target RNA. The potential use of synthetic hammerhead ribozymes as …
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Evolution and Engineering of RNA-based Macromolecular Machines
… world scenario would be an RNA “replicase” – a ribozyme capable of self-replication as well as copying other RNA sequences. While such a replicase has not been found in nature, past work in our laboratory identified artificial ribozymes that are promising candidates for further engineering …
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