Olivia Zou
Brandeis / Biological Physics
Hosted by Rogers' Lab
“Investigating Kinetics of Oligos Binding to DNA Secondary Structures”
Olivia Zou, W. Benjamin Rogers
Abstract
Ribonucleic acids (RNA) are molecules that rely on their three-dimensional structure to regulate many cell processes, such as delivering molecules or making proteins. Many viruses also have an RNA genome that helps in the assembly of their capsid shells. Therefore, disrupting the structure of RNA would help in the study of RNA function and antiviral therapy. One such way is to bind oligonucleotides to RNA, preventing the nucleic acid from folding into the structure required for it to function. However, this is a difficult task as the three-dimensional structure of RNA prevents DNA from binding stably. For this research, we aim to understand how hybridization kinetics of oligonucleotides binding to nucleic acid secondary structures depends on the type of secondary structure.
We start with designing a library of DNA secondary structures. DNA secondary structures are single stranded DNA that have regions of self-complementarity, allowing the strand to fold in on itself to create structures like hairpins, bulge loops, internal loops, pseudoknots, and junctions. Our initial designs are of hairpins, bulge loops, and internal loops with various loop and toehold lengths. The length of these features should result in different opening rates when an oligonucleotide binds to the structure. In addition, the position of free nucleotides on these structures, i.e., externally on the toehold or internally on the loop, should also affect opening rates. A universal probe with dye modifications binds to all these structures, allowing us to make fluorescent measurements of DNA species in solution.
Initial results with hairpins do not show a trend between toehold length and opening rates. Future work would involve understanding this lack of a trend and comparing the effects other features (such as loop length) have on opening kinetics.
Support: SMURF (Summer MRSEC Undergrad Research Fellowship)