Date of Award


Degree Name



College of Science

Type of Degree


Document Type


First Advisor

Bin Wang

Second Advisor

Michael L. Norton

Third Advisor

Leslie Frost


The expression of ferritin and amyloid precursor protein (APP) is post-transcriptionally regulated by iron-regulating proteins via binding to a stem-loop structure known as an iron-responsive element in the 5’-untranslated region (5’UTR) of ferritin and APP mRNAs. In this study, we used atomic force microscopy (AFM) to visualize the conformation of the 5’UTRs of ferritin heavy chain (Ferritin-H), ferritin light chain (Ferritin-L), and APP mRNA transcripts from human and mouse, and determined the secondary RNA structures using selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE). The AFM imaging did not provide high resolution structural information about these RNAs, whereas the SHAPE procedure successfully interrogated the secondary RNA structures at single nucleotide resolution. To our knowledge, this is the first time that the secondary structures of the entire 5’UTRs of these RNA molecules have been experimentally mapped. This study paves the way for the further investigation of RNA-ligand interactions in these RNA molecules.