Undergraduate Honors Theses

Thesis Defended

Spring 2013

Document Type



Chemistry & Biochemistry

First Advisor

Dr. Robert Batey


Riboswitches are elements that directly bind small molecule metabolites without the assistance of other factors. Riboswitches are found in the leader sequence of bacterial as well as some plant and fungi mRNA’s. They are highly specific towards the metabolite that they bind which helps them play a significant role in gene regulation. The S-denosylmethionine (SAM) sensing riboswitches modulates the expression of genes involved in the sulfur metabolism and methionine biosynthesis. One family of SAM sensing riboswitches that has been briefly studied by the Batey laboratory is the SAM-I/IV riboswitch. A preliminary structure was solved at 3.5 Å resolution. While this resolution was sufficient to generate a large amount of the model, a higher resolution image of the riboswitch is essential for visualizing the details of the AD-ligand complex. A high resolution image of this region is necessary in order to clearly see the binding mechanism of this complex, which will help us fully understand the directing structure-function studies on this RNA. This study was performed with the intent to find optimal crystallization conditions as well as to implement point mutations within the crystal construct to improve the resolution of the SAM-I/IV riboswitch structure. A molecular model was made that helped clarify important regions in the wild-type structure.