Targeting GC-Rich Quadruplex Structures in the Human Genome with Small Molecule Ligands

Xia, Ying (2022) Targeting GC-Rich Quadruplex Structures in the Human Genome with Small Molecule Ligands. Doctoral thesis, University of East Anglia.

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GC-rich DNA and RNA sequences can fold into a number of non-canonical structures such as G-quadruplexes and i-motifs. These structures have been shown to be able to affect many biological processes such as transcription, translation and replication. Targeting these sequences with small molecules can provide tools and leads for chemical intervention in these processes. This thesis describes the characterisation and interaction of compounds with GC-rich nucleic acids.

Chapter 1 is a general introduction to the research area of DNA secondary structures and focuses in particular on i-motif and G-quadruplex DNA, ligands, techniques used to study the folding and shape of these structures, and how to study melting curves of oligonucleotides.

Chapter 2 is the project of designing novel i-motif binding ligands and synthesis of a minor groove binder PyPyPyβDp. Another minor groove binder netropsin was also selected for DNA binding studies. Both minor groove binders were examined with i-motif, G-quadruplex and duplex DNAs using fluorescent intercalator displacement (FID) assay, fluorescence resonance energy transfer (FRET) melting and circular dichroism (CD) melting experiments. The results show these two minor groove binders can interact with the i-motif structure.

Chapter 3 is the work of exploring i-motif stabilizers using several biophysical techniques, including the FID assay, FRET melting and CD. Two NCI ligands 71795 and 19990 were found to stabilize the hTeloC i-motif. The metal complexes 22 and 23 can destabilize the i-motif structure. Iron cylinder was found to unfold the i-motif structure.

Chapter 4 is the work studying the interaction of TMPyP4 with RNA G-quadruplex. CD and UV titration experiments were used to examine the effect of TMPyP4 on PQS18-1 RNA G-quadruplex structure, and it can unfold the RNA structure. CD melting experiments were also used to investigate the thermal stability of PQS18-1 RNA G-quadruplex in the presence of ligands, and the results show TMPyP4 destabilizes the RNA G-quadruplex structure.

Chapter 5 begins with the characterization of GC-rich repetitive repeat sequences from the human genome. The sequences with the number of C and G-tracts from 3 to 5 were selected. The biophysical results show all these C-rich sequences can form intramolecular quadruplexes. With increased number of G-tracts, the proportion of parallel G-quadruplex topology also increased.

Chapter 6 provides a general conclusion, discussion about this work, and overviews for future works.

Chapter 7 describes the experimental procedures used in Chapters 2, 3, 4, and 5.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Pharmacy
Depositing User: Chris White
Date Deposited: 24 Oct 2023 10:50
Last Modified: 24 Oct 2023 10:50

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