Optimization of the Introduction of 2,6-Dimethylphenol at the C4-Atom of 2’-Deoxythymidine for the Preparation of Modified Oligonucleotides

Nucleic acids, including DNA and RNA, are vital for genetic information storage and expression, finding applications in diverse fields. Chemical synthesis is commonly used for nucleic acid modification, utilizing protecting groups to selectively modify specific positions without disrupting the overall structure. This study focuses on optimizing the introduction of a 2,6-dimethylphenoxy group at the C4 position of a protected 2’-deoxythymidine, a modification for enhancing stability, binding affinity, and expanding chemical diversity for future applications in therapeutics, diagnostics, and nanomaterials. Silylation was used as the initial step for 2’-deoxythymidine protection, followed by the preparation of the modified nucleoside. Optimization of synthetic procedures involved adjustments of reaction parameters, such as solvent and reagent stoichiometry, using small- and large-scale reactions. Extensive experimentation revealed that changing the solvent from tetrahydrofuran to dichloromethane and using 1,8-diazabicyclo [5.4.0] undec-7-ene as the base provided significant progress in reaction efficiency. Analytical techniques, including thin-layer chromatography and 1H Nuclear Magnetic Resonance spectroscopy, were employed for monitoring and confirmation of compound identity and purity. Successful optimization of the synthetic protocol will contribute to nucleic acid modification chemistry advancement with potential applications in therapeutics or diagnostics.