Manipulation of G-quadruplex nanostructures using sequence engineering and chemical modifications: towards development of functional G-quadruplex scaffolds

• Main Author: Singh, Abhishek
• Other Authors: Phan Anh Tuan
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2024
• Subjects: Chemistry; Biophysics
• Online Access: https://hdl.handle.net/10356/174782
• Institution: Nanyang Technological University

G-quadruplexes (G4s) are four stranded non-canonical nucleic acid structures made up of guanine (G) rich sequences. These structures are shown to exist inside the cells and play important roles in various crucial processes like gene expression, DNA replication, transcription and translation. Synthetic G4s are shown to have different functional applications in therapeutics and nanotechnology. However, design and development of these synthetic G4s for specific applications is far from trivial as it requires deeper understanding of controlling the G4 structures. Sequence engineering and chemical modifications are useful strategies in manipulating these structures and can be helpful in the development of G4s with desired properties. This dissertation is focused on the manipulation of G4 structures using sequence engineering and chemical modifications. It is further strategized towards the development of G4 as a functional scaffold. Specifically, in one project, we tried to control the assembly of G4 blocks using a G4 with a vacant site, and this assembly process further prompted us to design sequences that resulted in the formation of higher order structures like G-wires, that show potential applications in nanotechnology. Another project is focused on chemically manipulating the G4 structures by fine tuning the loops of intramolecular parallel three and four layered G4s by using acyclic synthetic linkers. Thermal stabilities studies on these modified structures indicated that the three and four layered G4 structures are most stable with seven and twelve covalent bonds in their central loops, respectively. Finally, we aimed towards the development of G4s as functional scaffolds that could show stimulate immune responses in cells. To this aim, we incorporated CpG (cytosine-phosphate-guanine) motifs in a loop of a parallel G4 forming sequence and studied its immuno-stimulatory properties in mouse macrophage cells.