Widom, JuliaHoeher, Janson2024-08-072024-08-072024-08-07https://hdl.handle.net/1794/29696RNA is an important biological molecule, with its function helping out with different processes in cells. How RNA functions is related to its structure, with different structured RNA behaving in different ways. Studying RNA structure is thus important to understand its function. One example of this are riboswitches, which help regulate gene expression. By binding a ligand, the riboswitch refolds, causing a change in gene expression. One method of studying RNA structure is by utilizing fluorescent base analogues of the native bases. To study the riboswitch, the fluorescent base analogue 2-aminopurine (2-AP) was substituted into six different locations in the L3 region of the preQ1 riboswitch. Using circular dichroism (CD) and fluorescence spectroscopy, along with fluorescence lifetimes, it was discovered that all modified locations were detrimental to the riboswitch’s ability to bind the ligand. In addition, fluorescence-detected circular dichroism (FDCD) was used to study short RNA molecules containing 2-AP, of up to three nucleotides in length. By comparing FDCD to CD, it was determined that in dinucleotides, the fluorescence came almost entirely from unstacked populations. Comparatively, while most of the fluorescence from the trinucleotide came from unstacked populations, some came from stacked populations. Through FDCD and CD, the amount of each construct in stacked and unstacked populations can be determined. This dissertation includes previously published co-authored material.en-USAll Rights Reserved.Electronic Thesis or Dissertation