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 11 of 11 for “"Pseudoknot"”.
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A Pseudoknot Improves Selection Efficiency in Ribosome Display
… improves stability of the complex, I tested a pseudoknot, originating from the genomic RNA of infectious bronchitis virus (IBV), a member of the positive-stranded coronavirus group. I used the previously-isolated anti-DNA scFv, 3D8, as a target protein. During in vitro translation in rabbit …
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Crystal structure and functional studies of a viral RNA pseudoknot involved in ribosomal frameshifting
Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999.
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FUNCTIONAL ANALYSIS OF THE UPSTREAM PSEUDOKNOT DOMAIN AND ITS SUBSTITUTION WITH A POLY(A) TRACT IN TOBACCO MOSAIC VIRUS (TMV)
THE UPSTREAM PSEUDOKNOT DOMAIN (UPD) OF TOBACCO MOSAIC VIRUS (TMV) GENOME PLAYS AN IMPORTANT ROLE DURING VIRUS REPLICATION AND TRANSLATION. THE FUNCTIONS OF UPD WERE ANALYZED USING A SUBSTITUTED MUTANT TMV-43A IN WHICH AN INTRODUCED 43 NT POLY(A) TRACT REPLACED THE UPD IN TMV GENOME. TMV-43A …
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BIOINFORMATICS INVESTIGATION OF RNA PSEUDOKNOTS
Pseudoknots are a special kind of RNA structures that play functional roles in a wide variety of biological processes. Pseudoknots are best known for their involvement in the −1 programed ribosomal frameshifting (−1 PRF) and stop codon readthrough translational recoding events as the stimulatory …
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Data mining in computational proteomics and genomics
… second part of this dissertation focuses on RNA pseudoknot structure matching and alignment. RNA pseudoknot structures play important roles in many genomic processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little …
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Analytic Combinatorics Applied to RNA Structures
… system. γ-structures are a subset of RNA pseudoknot structures filtered by topological genus that lend themselves nicely to combinatorial analysis. Namely, the coefficients of their generating function can be approximated for large n. This paper is an investigation into the length-spectrum …
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STRUCTURAL STUDY OF HUMAN CATENIN ΒETA-LIKE PROTEIN 1 AND DOUBLE RNA PSEUDOKNOTS IN -1 RIBOSOMAL FRAMESHIFTING
… especially AID. Project 2 -- study of double pseudoknots in the regulation of -1 programmed ribosomal frameshifting in RNA viruses −1 programmed ribosomal frameshifting (PRF) is utilized by many viruses to synthesize their enzymatic and structural proteins at a defined ratio. For efficient −1 …
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Design and implementation of a cyberinfrastructure for RNA motif search, prediction and analysis
… a random forest classification algorithm, a pseudoknot removal algorithm, and a feature ranking algorithm based on the gini impurity measure. A series of experiments including 10-fold cross- validation has been conducted to evaluate the performance of the Junction-Explorer tool. Experimental …
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Point mutational examination of eukaryotic initiation factor 4E (eIF4E), inclusion bodies analysis, and Barley Yellow Dwarf Virus (BYDV) exonuclease resistant RNA structure mapping and prediction
… stem loop. The C-rich and G-rich regions form a pseudoknot where the G-rich region contains a flexible G that is thought to flip outward and potentially act as a 5’ m7GTP cap analog to bind eIF4E. Point mutations were introduced into wheat eIF4E in order to identify amino acids needed for PTE …
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Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression
… frameshifting is directed by a downstream RNA pseudoknot structure, to facilitate expression of the ORF1b-encoded viral replicase. At a second PRF site, both −1 and −2 PRF are stimulated by a trans-acting complex of a viral (nsp1β) and cellular (PCBP) protein in a unique, non-canonical …
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Computational studies of the structure, dynamics, and catalysis of the hepatitis delta virus ribozyme
… The HDV ribozyme has a compact double-pseudoknot structure and uses a combination of metal ion and nucleobase catalysis to effect its self-cleavage reaction. An active site cytosine C75 is thought to act as a general acid in the catalytic reaction by donating a proton to the 5’-hydroxyl …