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 21 for “"RNA Interaction"”.
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A GPU accelerated RNA-RNA interaction program
RNA-RNA interaction (RRI) is important in processes like gene regulation, and is known to play roles in diseases including cancer and Alzheimer's. Large RRI computations run for days, weeks or even months, because the algorithms have time and space complexity of, respectively, O(N3M3) and O(N2M2), …
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A Combinatorial Framework for Multiple RNA Interaction Prediction
<p>The interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. However, biological mechanisms in which more than two RNAs take part in an interaction also exist.</p> <p>A typical algorithmic …
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Modulation of West Nile Virus Capsid Protein and Viral RNA Interaction through Phosphorylation
… are unknown. This study aims to characterize the interaction between WNV viral RNA and the capsid (C) protein and also elucidate how the processes of nucleocapsid assembly are regulated. Initial in vitro C protein and viral RNA interaction studies showed that this interaction was not specific. …
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Investigation of Ribosome Structure and Ribosome-Transfer Rna Interaction Using T4 Rna Ligase
T4 RNA ligase can be used to alter the sequence of E. coli ribosomal RNAs in the intact polyribosome, ribosome and subunits. This enzyme will catalyze the addition of a 3',5'-bisphosphate onto the 3' terminus of rRNAs resulting the rRNA molecules one nucleotide longer with a 3' phosphate. The RNA …
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Engineered mRNA regulation using an inducible protein-RNA aptamer interaction
… of naturally occurring regulation of RNA function in biology is increasingly being recognized. A common regulatory mechanism uses inducible protein-RNA interactions to shape diverse aspects of cellular RNA fate. Recapitulating this using a novel set of protein-RNA interactions is …
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Identification of novel transcripts in hepatocellular carcinoma using RNA-seq
… helped the finding of novel transcripts by deep RNA sequencing (RNA-Seq). The approach to identify novel transcripts using RNA-Seq has been studied, however, prediction of their functional roles in cancers are not studied thoroughly. Here, I constructed new pipeline to identify putative novel …
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Casting Protein Structure Predictors as Energy-Based Models for Binder Design and Scoring
… In this work, we propose a principled alternative: an energy-based framework that directly extracts the statistical likelihood of a predicted binder–target complex from a structure predictor’s internal confidence distributions. Building on the Joint Energy-based Modeling (JEM) framework, we …
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Single molecule pull down of double strand RNA binding proteins
RNA molecules are transcribed as single stranded naturally, but with most of them forming in to structures composed of duplex regions, loop, bulge or mismatches. RNAs with double stranded regions, or known as double-strand RNAs (dsRNAs). The class of proteins responsible for processing dsRNAs is …
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New Microfluidic Technologies for Studying Histone Modifications and Long Non-Coding RNA Bindings
… histone modification, and non-coding RNA interaction, play critical roles in cell differentiation and disease processes. The conventional approach requires the use of a few million or more cells as starting material. However, such quantity is not available when samples from patients …
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Biochemical Analysis of Evolutionary Divergent Vertebrate Larp6 Proteins
… proteins (LARPs) contain a conserved bipartite RNA binding domain, called the La module, which consists of the La motif and an RNA recognition motif (RRM). Across the LARP subfamilies, the La module interacts with a variety of RNAs, allowing this protein superfamily to perform roles as chaperone …
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Tap /Nxf1 N -Terminal Domain Mediates Homotypic Complex Assembly and Is Necessary for Nuclear RNA Export
… nuclear export receptor for both poly (A+) RNA as well as cellular and viral RNAs containing the constitutive transport element (CTE). Tap is a multi-domain protein that interacts directly with nucleoporin proteins of Nuclear Pore Complexes (NPCs) as well as messenger RNA cargo. It has been …
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Structure determination of a yeast ribosomal protein L30 and pre-mRNA binding site complex by NMR spectroscopy
… protein L30 and its auto-regulatory pre-mRNA binding site provide one of the best examples the critical role of protein-RNA interactions in regulation of RNA processing and control of gene translation. A model system for this interaction, which includes the ribosomal L30 protein and the …
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Computational Modeling of Rna-Small Molecule and Rna-Protein Interactions
<p>The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive …
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The evolution, modifications and interactions of proteins and RNAs
Proteins and RNAs are two of the most versatile macromolecules that carry out almost all functions within living organisms. In this thesis I have explored evolutionary and regulatory aspects of proteins and RNAs by studying their structures, modifications and interactions. In the first chapter of …
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The Interaction Between Eukaryotic Translation Initiation Factor eIF4G and 3’ Cap Independent Translation Element of Barley Yellow Dwarf Virus Is Affected by Multiple Initiation Factors
… in the 3’ untranslated region of the viral mRNA. BTE (Barley Yellow Dwarf Virus like cap-independent translation element) is one of the well characterized CITEs. BTE mediated translation primarily depends on eukaryotic initiation factor eIF4G. BTE binds to eIF4G; however, the details of BTE …
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Bioinformatic methods for analyses of epigenome and RNA interactome
… is far from complete, particularly on non-coding RNAs and regulatory sequences. Epigenomic modifications and variations were considered to contribute to the diversity of functions found across different cell types, play key roles in the establishment and maintenance of cellular identity during …
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Unraveling the interactions between MBNL1 protein and its RNA targets
The muscleblind-like protein 1 (MBNL1) is an RNA binding protein with four conserved zinc fingers that plays an important role in the regulation of alterative splicing. It interacts with pre-mRNA and promotes the inclusion or exclusion of exons to form different mRNA transcripts. Besides its …
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Investigation of the interactions in RNA recognition motif-RNA complexes: small molecule inhibitors and kinetics of dissociation
The RNA recognition motif (RRM) is the most abundant RNA binding domain that is found in all organisms. RRM-containing proteins participate in most steps of gene expression, including translation, splicing, modification and transport of RNA. This dissertation aims to help understand the …
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Characterization of a single TRAM domain RNA-binding protein from the Antarctic methanogen Methanococcoides burtonii
… to nucleic acid binding, including specific interactions describing putative roles of Ctr3 in the cell. During purification, E. coli nucleic acids consistently co-purified with recombinant Ctr3. The liberated nucleic acid from proteins was able to be digested with RNase indicating the bound …
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Apobec-1 Complementation Factor (ACF) Binds and Regulates Multiple RNAs
AU-Rich Elements: ARE) are cis-acting RNA sequences in the 3'UTRs of a wide range of transcripts that function to regulate mRNA stability, localization, and/or translation through interaction with ARE-Binding Proteins. Apobec-1 Complementation Factor: ACF) was originally identified as a co-factor …
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