Fluorescent Modified Nucleosides and Their Impact on Structure and Function of a Model Aptamer
A number of non-natural nucleic acid monomers were synthesized and employed in a model system in an effort to demonstrate the potential for expanding the chemical repertoire of previously known functional nucleic acids. Aptamers, a type of functional nucleic acids capable of target-specific binding, have been employed in a variety of applications which take advantage of their functionality offered by the structures formed as a result of their intramolecular interactions. These interactions are the basis of the formation of structures such as the G-quadruplex, a structure composed of stacked guanine-tetrads, which is adopted by a well-studied model aptamer for thrombin. The synthesis of modified guanine probes, 8-(4ʹʹ-styryl)-2ʹ-dG (StydG), 8-(4ʹʹ-cyanostyrene)-2ʹ-dG (CNdG), as well as modified 5-furyl-2′-deoxyuridine (FurdU) are presented in this thesis. The investigations herein detail the synthesis and incorporation of modified nucleic acids into this model aptamer, TBA, thereby demonstrating the effects of expanding the chemical repertoire on functionality, as determined by parameters such as binding, fluorescence, and stability.