First Advisor

Rahul Raghavan

Date of Award


Document Type


Degree Name

Bachelor of Science (B.S.) in Chemistry and University Honors




Riboswitches -- Analysis, Genomics, RNA-protein interactions




Riboswitches are RNA molecules that regulate gene expression, without the need for protein factors, at the mRNA level in the bacterial kingdom. This paper focuses on nine riboswitches: TPP, FMN, SAM, Lysine, Cobalamine, Glycine, Molybdenum, Mg, and SAH, and whether or not there exists a relationship between genome size and riboswitch existence. The hypothesis of this paper is that there does exist a direct relationship because it is assumed that the more basepairs (bp) in a genome, the higher the chance that an old characteristic, such as a riboswitch, is conserved. Three hundred twenty members of the gammaproteobacteria class were selected using the Rfam and NCBI databases, and grouped by genome size. Each group was then analyzed via direct counting correlation and one way ANOVA for correlation and covariance. To check ANOVA assumptions, the gammaproteobacteria were grouped according to their respective genus ancestry, and statistics similarly ran. The Method of Most Likelihood was run for both sets via SPSS. The hypothesis of this paper was wrong. A direct, highly correlative relationship between genus ancestry and riboswitch existence was determined; whether or not each riboswitch was present or absent in the gammaproteobacteria analyzed was dependent upon whether the individual bacteria belonged to a genus that had that characteristic. A potential, stricter relationship between species and riboswitch existence was discovered, leaving room for further movement in this research.


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An undergraduate honors thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in University Honors and Mathematics and Chemistry

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