Poster abstracts

Poster number 79 submitted by Marla Gravino

Into the Unknown: Covalently Targeting RNA with Electrophilic Warheads

Marla R. Gravino (University of Notre Dame Department of Chemistry & Biochemistry), Adam B. Wier (University of Notre Dame Department of Chemistry & Biochemistry), Nya S. Huff (University of Notre Dame Department of Chemistry & Biochemistry), Dr. Brittany S. Morgan (University of Notre Dame Department of Chemistry & Biochemistry)

Abstract:
RNA is widely recognized for its role as a messenger in the central dogma. However, most RNA is non-coding and is largely understudied as structural, functional, and therapeutic characterization remains challenging. Though small molecules are useful tools to probe these properties, RNA is particularly challenging to target with traditional non-covalent ligands due to its dynamic nature. To overcome challenges with RNA dynamics, covalent chemistry can be utilized as RNA nucleotides contain nucleophilic positions that can react with electrophilic warheads, such as the 2’-hydroxyls that react with SHAPE reagents. Reacting RNA nucleotides with electrophiles will allow for a better understanding of reactivity with RNA. However, canonical and commercially available RNA nucleotides (NMPs) do not mimic RNA due to differences in the phosphate charges and the presence of a 3’-hydroxyl group. To address this gap, I designed RNA nucleotide mimetics that model the electronic environment of RNA; they contain ethylated phosphates with a -1 charge on both the 3’- and 5’-positions to mimic the charge state of an oligonucleotide while the ethyl groups mimic the “turn” of an additional nucleotide. Once synthesized, I will react these molecules in vitro with a library of diverse electrophiles and measure covalent bond formation by LC/MS. I will then utilize HPLC to quantify percent covalent bond formation of each reaction and NMR to identify where covalent bond formation occurred. I expect this screen to provide insights into RNA nucleotide reactivity, opening the door to capturing RNA selectively and elucidating the functions of this biological enigma.

Keywords: electrophile , covalent , modified nucleotide