Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry

Optimized and stringent chemical methods to profile nascent RNA expression are still in demand. Herein, we expand the toolkit for metabolic labeling of RNA through application of inverse electron demand Diels-Alder (IEDDA) chemistry. Structural examination of metabolic enzymes guided the design and synthesis of vinyl-modified nucleosides, which we systematically tested for their ability to be installed through cellular machinery. Further, we tested these nucleosides against a panel of tetrazines to identify those which are able to react with a terminal alkene, but are stable enough for selective conjugation. The selected pairings then facilitated RNA functionalization with biotin and fluorophores. We found that this chemistry not only is amenable to preserving RNA integrity but also endows the ability to both tag and image RNA in cells. These key findings represent a significant advancement in methods to profile the nascent transcriptome using chemical approaches.

Tunable reactivity of geminal bis(silyl) enol derivatives leading to selective exo-IEDDA or Sakurai allylation with a β,γ-unsaturated ketoester

Two contrasting pathways in a SnCl4-catalyzed reaction of geminal bis(silyl) enol derivatives with β,γ-unsaturated ketoesters have been achieved by tuning the R group in the enol moiety. While the electron-donating Bn-substituted enol ether undergoes an exo-selective inverse-electron-demand Diels-Alder (IEDDA) reaction to give dihydropyran, the electron-withdrawing Ac-substituted enol ester reacts as an allylsilane to provide a Sakurai-allylated product with predominant syn-selectivity.