Abstract
RNAs are molecules that rely on their 3D structure to regulate cell processes, such as delivering molecules or making proteins. Therefore, disrupting the structure of RNA could help us better understand or even modulate these functions. In principle, one way to do this is to bind DNA oligonucleotides to the RNA to change its conformation so that it no longer functions. In practice, this is a difficult task as the complex secondary and tertiary structures of RNA often prevent DNA from binding stably. We aim to understand how kinetics of oligo binding to a secondary structure depends on the type of secondary structure. We design a set of hairpins, bulge loops, and internal loops with various loop and toehold lengths. A fluorescent probe binds to all these structures, allowing us to make measurements of the amount of unfolded molecules. Preliminary results show that reaction rates increase with increasing external toehold length for all structures.