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Title: Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes

The structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl 2, ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. This method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. Our research demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules.
Authors:
 [1] ;  [1] ;  [1]
  1. National Inst. of Health (NIH), Bethesda, MD (United States)
Publication Date:
OSTI Identifier:
1229899
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature Communications; Journal Volume: 6; Journal Issue: 12
Publisher:
Nature Publishing Group
Research Org:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org:
National Inst. of Health (NIH), Bethesda, MD (United States)
Country of Publication:
United States
Language:
ENGLISH
Subject:
biological sciences; biophysics; molecular biology