Date of Award

Spring 2024

Document Type

Restricted Thesis

Terms of Use

© 2024 Harrison Kim. All rights reserved. Access to this work is restricted to users within the Swarthmore College network and may only be used for non-commercial, educational, and research purposes. Sharing with users outside of the Swarthmore College network is expressly prohibited. For all other uses, including reproduction and distribution, please contact the copyright holder.

Degree Name

Bachelor of Arts

Department

Chemistry & Biochemistry Department

First Advisor

Liliya A. Yatsunyk

Abstract

A single strand of guanine-rich DNA can fold into a non-canonical four stranded secondary structure called the G-quadruplex (GQ) where guanines arrange into guanine tetrads via Hoogsteen hydrogen bonds. GQs can fold into either right- or left-handed helical conformations. The left-handed conformation is quite novel and has not been characterized extensively. We have characterized a lefthanded minimal motif (GGTGGTGGTGTG) that is found as a transcript variant in the KRAS proto-oncogene on chromosome 11. The KRAS gene is an important target as the protein it encodes is essential to the RAS/MAPK signaling pathway and is challenging to target with cancer therapeutics due to the protein’s small size. Biophysical techniques like circular dichroism, UV-Vis melting, and native PAGE were used to characterize the conservation and stability of left-handedness with the addition of nucleotides to the KRAS motif. Our data indicate that the addition of nucleotides disrupts left-handedness and that the left-hand construct has a complex UV-Vis melting profile with high hysteresis. The interactions between a left-handed KRAS variant and GQ-stabilizing small-molecule ligands like NMM, Braco19, and PhenDC3 were also characterized using similar biophysical techniques. NMM, Braco19, and PhenDC3 all confer a right-handed helicity to left-handed KRAS sequences. NMM, a selective ligand for parallel GQs, binds weakly (Ka = 0.124 ± 0.009 μM-1) and with a 1:1 binding stoichiometry. This work seeks to understand the conditions in which left-handed GQs form, the targeting of left-handed GQs with small-molecule ligands, and the biological relevance of left-handed GQs.

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