Date of Award
Spring 2026
Document Type
Thesis
Terms of Use
© 2026 Eric Xing. This work is freely available courtesy of the author. It may be used under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license. For all other uses, please contact the copyright holder.
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Degree Name
Bachelor of Arts
Department
Chemistry & Biochemistry Department
First Advisor
Liliya A. Yatsunyk
Abstract
G-quadruplexes (G4s) and i-motifs (iMs) are noncanonical DNA structures associated with G- and C-rich DNA sequences, respectively. Their location in telomeres and oncogene promoters makes them promising anticancer targets. While most G4s have a right-handed (RH) fold, there also left-handed (LH) G4s, whose formation and interaction with RHG4-specific ligands is poorly understood. LHG4s are sequence dependent and form only by two minimal motifs, M1, G(TGG)3TG, and M2, (GGT)3GTG. Here, we use biophysical and X-ray structural methods to characterize LHG4s and iMs. We first characterized a G4 containing both LH and RH subunits (LH/RHG4) from the SLC2A1 oncogene promoter, testing additions of nucleotides in the 5′- and 3′-direction from its genomic context and its interactions with RHG4 ligand, N-methylmesoporphyrin IX (NMM). We found that 3’ addition of C/CA does not alter the LH fold, but 5’ addition of G does. To address whether the side or identity of the addition is disruptive, we designed four sequences, M1M1, M2M2, M1M2, and M2M1, based on the minimal LH motifs. We added A, T, C, or G to either the 5’ or 3’ ends. All four sequences were sensitive to additions of G, while only M2M1 tolerated both 5’ and 3’ additions of A, T, or C. We also solved five crystal structures: two LHG4s (M1M2; M2M1) and three LH/RHG4s (M1M2; 2 for M1M2-3T). Addition of NMM caused conversion to RHG4s for all sequences, but a crystal structure of a LH/RHG4 variant (M1M2-5T) revealed NMM binding to both LH and RH subunits. Regarding iMs, we solved the crystal structure of an iM from the HIF-1α oncogene promoter. This is only the second crystal structure of a biologically relevant iM. The HIF-1α iM displays multiple forms with a conserved iM core containing 7 C-C+ base pairs and three different capping interactions (C+-C, C-G, and C+-G).
Recommended Citation
Xing, Eric , '26, "Biophysical and X-ray Crystallographic Characterization of Noncanonical DNA Structures" (2026). Senior Theses, Projects, and Awards. 1054.
https://works.swarthmore.edu/theses/1054