Dissertation/Thesis Abstract

Using RNA Mimicry of Viroids to Uncover New Noncoding RNA Structural Motifs and Pathways
by Freidhoff, Paul, Ph.D., University of the Sciences in Philadelphia, 2020, 186; 27665966
Abstract (Summary)

There is broad interest in ncRNAs within technology. The functions of ncRNAs are linked to RNA structural elements, but most of the structure-function relationships of ncRNAs are unknown, which limits the use RNA in technology.

Viroids are the first ncRNAs observed. They are unique pathogens because they exclusively hijack ncRNA pathways by mimicking structures found in cellular RNAs. This makes viroids excellent models to study structural-functional relationships of cellular ncRNAs.

In this research, we studied a structural element, the sarcin/ricin domain motif, found in PSTVd. This structural element is important in replication and processing, but the same structural element was not found in all viroids belonging in the Pospiviroidae family (a family of biochemically related viroids) using traditional methods including secondary structure prediction.

Viroids in the Pospiviroidae utilize similar biochemical pathways including replication and RNA processing pathways. Furthermore, they utilize similar cellular factors in the processing and replication pathways so we have hypothesized that every Pospiviroidae forms a similar structural element like an SRD. We used computational methods including alignment, molecular dynamics, and RNA footprinting to show that every Pospiviroidae could form an SRD-like motif. The work also suggests that there could be undiscovered subsets of SRD mimics. The knowledge of conserved structural elements in RNA processing could be applied in RNA technology.

In addition to structural analysis, our work resulted in the development of new analysis methods. These included an enrichment method to remove large RNAs from an RNA mixture without the removal of small to moderate sized RNAs. We have also progressed in developing a new cell-based RNA assay which will analyze the effects of cellular biochemical factors on viroid processing.

Indexing (document details)
Advisor: Bruist, Michael F.
Commitee: Baird, Nathan J., Klase, Zachary A., Zauhar, Randy J., Gianti, Eleonora
School: University of the Sciences in Philadelphia
Department: Biochemistry
School Location: United States -- Pennsylvania
Source: DAI-B 81/6(E), Dissertation Abstracts International
Subjects: Biochemistry, Chemistry
Keywords: Molecular dynamics, Noncoding RNA, Replica exchange molecular dynamics, RNA structure, Sarcin/ricin motif, Viroid
Publication Number: 27665966
ISBN: 9781392819623
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