Investigating the Interactions of Poly(A)-Coralyne in Crowded Environments and the Effect of DNA Methylation on DDD-Lysine and DDD-Arginine Interactions

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Zeynep_Suvaci_Thesis.pdf

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2022-1

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Suvacı, Zeynep

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Poly(A) tail is an essential determinant of mRNA stability and maturation and is required for translation initiation. Small molecules recognizing poly(A) tails might interfere with mRNA processing. Hence, they have the potential to act as therapeutic agents. Coralyne (COR), a strong poly(A) binder, is shown to induce the formation of a stable, double-stranded poly(A) self-structure under dilute solution conditions. Although studies in dilute solutions are very informative, they do not necessarily reflect DNA structure and stability in vivo. Within the first part of this thesis, poly(A)-COR interactions under molecular crowding conditions were investigated to shed light on the behavior of poly(A)-COR in intracellular environments. PEG200, sucrose, and glycerol were used to mimic the cellular environment. Results of thermal denaturation experiments revealed a decrease in poly(A)-COR stability, especially with increasing PEG concentration. CD spectroscopy results confirmed that while the characteristic spectrum of poly(A)-COR was conserved, it was altered slightly in the presence of crowding agents, especially PEG. In the second part of this thesis, the effect of DNA methylation on the interactions of Dickerson Dodecamer (DDD) with lysine (Lys) and arginine (Arg) amino acids, which are profoundly found in histones, was investigated. The methylation of cytosines at the 5th position (d5mC) is one of the most common epigenetic modifications and is believed to alter gene expression. CD spectroscopy results revealed the conservation of B-form structure upon DNA methylation. Increasing the amino acid concentrations is found to alter the B-DNA structure, where the effect was noteworthy in the unmethylated DDD compared to DDD8, which has 8 methylated cytosines. In addition, the effect of Arg on DNA stability was found to be more substantial compared to Lys via UV-Vis thermal denaturation experiments.

Subject Keywords

Poly(A), Coralyne, Molecular Crowding, DNA Methylation, Dickerson Dodecamer

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https://hdl.handle.net/11511/96062

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Graduate School of Natural and Applied Sciences, Thesis

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Citation Formats

Z. Suvacı, “Investigating the Interactions of Poly(A)-Coralyne in Crowded Environments and the Effect of DNA Methylation on DDD-Lysine and DDD-Arginine Interactions,” M.S. - Master of Science, Middle East Technical University, 2022.