Characterization of Conformational Dynamics of Bistable RNA by Equilibrium and Non‐Equilibrium NMR

Fürtig, Boris; Reining, Anke; Sochor, Florian; Oberhauser, Eva Marie; Heckel, Alexander; Schwalbe, Harald

doi:10.1002/0471142700.nc1113s55

Cited by 1 publication

(1 citation statement)

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“…Weighted average chemical shift perturbations (CSP) were calculated using the equation \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\sqrt {{\mathrm{\Delta }}{{\mathrm{H}}}^2 + 0.1{\mathrm{\Delta }}{N}^2}$\end{document} ( 37 ). Imino resonances of SL3a and SL3e states from 1 H– 15 N HSQC spectra were used to determine populations from peak integration following established protocols ( 38 ) at 25°C (residues U247, G252, G253, G259) and 37°C (residues G252, G253).…”

Section: Methodsmentioning

confidence: 99%

Visualizing a two-state conformational ensemble in stem–loop 3 of the transcriptional regulator 7SK RNA

Camara,

Lange,

Yesselman

et al. 2023

Nucleic Acids Research

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Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem–loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows either or both states are highly conserved. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.

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Section: Methodsmentioning

confidence: 99%