Binding of oligos to DNA secondary structures

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 works. 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 the kinetic and thermodynamic reasons why oligonucleotides fail to bind to secondary structures. In this talk, I will describe a series of experiments investigating the binding of short DNA oligonucleotides to nucleic acids with prescribed secondary structures. We design a set of hairpins, bulge loops, and internal loops with various loop and toehold lengths, which should result in different opening rates when the oligo binds. A fluorescent probe binds to all these structures, allowing us to make measurements of the amount of unfolded molecules. Preliminary results show that opening rates of different secondary structures vary by orders of magnitude, with hairpins being fastest, and internal loops being slowest.