Investigating hybridization kinetics of oligos binding to DNA secondary structures

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dc.contributor.advisor Rogers, W. Benjamin
dc.contributor.advisor Kondev, Jané
dc.contributor.author Zou, Olivia
dc.date.accessioned 2019-05-14T15:40:10Z
dc.date.available 2019-05-14T15:40:10Z
dc.date.issued 2019
dc.identifier.uri https://hdl.handle.net/10192/36657
dc.description.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. en_US
dc.format.mimetype application/pdf en_US
dc.language English
dc.language.iso en en_US
dc.publisher Brandeis University
dc.relation.ispartofseries Brandeis University Theses and Dissertations
dc.rights Copyright by Olivia Zou 2019 en_US
dc.title Investigating hybridization kinetics of oligos binding to DNA secondary structures en_US
dc.type Thesis en_US
dc.contributor.department Undergraduate Program in Biological Physics
dc.degree.name BS
dc.degree.level Bachelors
dc.degree.discipline Biological Physics
dc.degree.grantor Brandeis University, School of Arts and Sciences


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