Book excerpt: Nucleic acids have been studied extensively due to their numerous functional roles in biological systems. Biological processes associated with the post transcriptional modification of RNA, namely RNA interference (RNAi) and RNA editing, have shown therapeutic potential due to their ability to alter mRNAs. RNA interference is a process which results in the cleavage of mRNA transcripts using a guide RNA template to find its target sequence and prevent translational expression. RNA editing causes the recoding of mRNA transcripts, altering protein function. The following dissertation discusses experiments which guide the chemical modification of RNA substrates of RNAi and RNA editing to bypass hurdles associated with their development as therapeutics. The Beal lab studies nucleobase modifications of short interfering RNAs (siRNAs), which are used in RNAi to target mRNA sequences of interest. Chapters 2 and 3 of this thesis will discuss nucleobase modifications to bypass the innate immune response of the cell and prevent off-target knockdown of undesired mRNA sequences. Using the crystal structures of an innate immune signaling protein, Toll-like Receptor 8 (TLR8), and of the catalytic endonuclease of RNAi, Argonaute 2 (Ago2), new chemical modifications for siRNAs were synthesized which can bypass TLR8 recognition and allow selective target mRNA cleavage by Ago2. Crystal structures of TLR8 bound to a small molecule and RNA derived agonists allowed the rational design of major and minor groove nucleobase modifications for siRNAs to bypass TLR8 recognition. To study the off-target knockdown of mRNA transcripts by Ago2, ethynyl modified riboses and nucleobases within key positions of the siRNA sequence were synthesized. Crystal structures of guide RNA loaded hAgo2 bound to an off-target mimic were vital for the study of these new triazoles. This resulted in the development of new siRNAs which were able to select for the knockdown of their targeted sequence over known off-target sequences. Chapter 4 of this dissertation discusses preliminary work in the use of small molecule molecular docking software to find nucleobase modifications to enhance RNA/protein interactions. New RNAs which can bind to guide strand loaded Ago2 were synthesized using this screening method and were found to bind more tightly than three of the four canonical RNA bases. This screening method was also applied to the RNA editing protein adenosine deaminase acting on RNA 2 (ADAR2). The recently solved crystal structure of ADAR2’s catalytic domain bound to its RNA substrate displayed a potential binding pocket to which modified, non-edited RNAs could bind. This work discusses the preliminary results of these modified non-edited RNAs, and how they influence the deamination reaction of ADAR2. This chapter also discusses the use of the transition state inhibitor 8-aza-nebularine from the solved crystal structure, as a ligand to accomplish a molecular docking screen to search for potential inhibitors of ADAR2.