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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Computer Simulations of RNA Replication in Protocells

Sanders, Quentin January 2024 (has links)
The RNA world hypothesis posits that at some stage in the development of life, RNA functioned as both an informational polymer and a catalyst for important reactions. However, many questions remain as to how RNA molecules might have evolved into living organisms. This thesis uses computer simulations to model processes thought to be important to the development of an RNA world. First, a model is discussed which describes non-enzymatic polymerization of single-stranded RNA from different kinds of activated nucleotides, a necessary first step towards an RNA world. It was found that a system undergoing polymerization of RNA from 5′-activated triphosphates or imidazolides behaves differently from an equilibrium system undergoing reversible polymerization reactions from 2′,3′-cyclic monophosphates, for example. In the 5′-triphosphate case, the system is not in equilibrium but rather in a state of circular reaction flux that must be maintained by an external source of phosphates. This model is then adapted to investigate non-enzymatic template-directed replication of RNA strands. It is found that this process fulfills all the necessary requirements to function as a metabolism which maintains a difference between the outside non-living environment and the internal environment of the cell. Finally, byproducts arising from the template copying mechanism in this model are discussed, including the development of highly regular sequence patterns in the strand population due to selection for the ability to form duplexes with neighbouring strands. Altogether, this thesis illustrates new implications, potential pitfalls, and possibilities of the RNA world hypothesis for the origin of life. In particular, it emphasizes the fundamental link between the processes of replication and metabolism, both of which must have been crucial to the functioning of the earliest protocells. This link has been largely overlooked in scientific literature on the topic to date. / Thesis / Master of Science (MSc) / For millennia, humanity has told stories about the origin of life. Since the 1960s, scientists have hypothesized that RNA is a key player in this origin story. RNA can both hold information and catalyze chemical reactions, meaning only one molecule is needed for both these crucial functions. However, many questions remain about how this would work in practice. This project used computer simulations to model steps along the path from RNA to living organisms. First, a model was developed for the formation of single-stranded RNA from building block molecules. The model was then expanded to include copying of existing RNA strands, and it was found that this process constitutes a metabolism. Finally, it was discovered that over time the copying process produces simple patterns in the sequence of building blocks that make up the RNA strands. Altogether, these findings emphasize the link between replication and metabolism in early cells.

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