Synthesis of a Chemical Probe for RNA Aptamer

Corbo, Holli Fay
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Aptamers are short single-stranded oligonucleotide molecules that can bind at site-specific sequences of a desired target. Synthetically synthesized chemical probes allow researchers to monitor site-specific interactions of RNA aptamers. However, probes of quality are difficult to produce and require substantial resources and funding. In this study, we develop a chemical probe for intended use in conjunction with Peppers, a promising RNA aptamer (Chenn et al., 2019). (4-((2-hydroxyethyl)(methyl)amino)-benzylidene)-cyanophenyl-acetonitrile (HBC), was synthesized in a series of 5 steps; reduction of a carboxylic acid by LAH to yield a primary alcohol, mild oxidation with DMP, Knoevenagel Condensation with an aldehyde and cyano-compound, N-alkylation, and deprotection. This aromatic acetonitrile is an electron acceptor that maintains rigidity and molecular structure for specific binding with Peppers. High binding affinity and thermal stability of this probe are advantageous compared to previously developed probes. The target molecule is desirable as it offers imaging of live cellular RNAs and their complex chemical nature in vivo (e.g., splicing, degradation, translocation.)