Probing RNA Conformational Equilibria within the Functional Cellular Context.

Journal Article (Journal Article)

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

Full Text

Duke Authors

Cited Authors

  • Ganser, LR; Chu, C-C; Bogerd, HP; Kelly, ML; Cullen, BR; Al-Hashimi, HM

Published Date

  • February 25, 2020

Published In

Volume / Issue

  • 30 / 8

Start / End Page

  • 2472 - 2480.e4

PubMed ID

  • 32101729

Pubmed Central ID

  • PMC7941409

Electronic International Standard Serial Number (EISSN)

  • 2211-1247

Digital Object Identifier (DOI)

  • 10.1016/j.celrep.2020.02.004


  • eng

Conference Location

  • United States