Probing RNA Conformational Equilibria within the Functional Cellular Context

• DOI: 10.1016/j.celrep.2020.02.004
• Publication Date: 2020-02-25T15:58:20Z
• Authors: Laura R. Ganser; Chia-Chieh Chu; Hal P. Bogerd; Megan L. Kelly; Bryan R. Cullen; Hashim M. Al-Hashimi
• Keywords: 0303 health sciences; 03 medical and health sciences; HEK293 Cells; Cellular Microenvironment; QH301-705.5; Cells; RNA Stability; Humans; Nucleic Acid Conformation; Biology (General); Genes, env; HeLa Cells

Low-abundance short-lived non-native conformations referred to as excited states (ESs) are increasingly observed in vitro and implicated the folding biological activities of regulatory RNAs. We developed an approach for assessing relative abundance RNA ESs within functional cellular context. Nuclear magnetic resonance (NMR) spectroscopy was used estimate degree which substitution mutations bias conformational equilibria toward inactive ES vitro. The activity ES-stabilizing mutants indirect measure Compensatory that restore ground-state conformation were control changes sequence. Using this approach, we show two RNAs from HIV-1, transactivation response element (TAR) Rev (RRE), likely form cells with abundances comparable those measured vitro, their targeted stabilization may provide avenue developing anti-HIV therapeutics.