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

Journal Article · Mon Dec 07 00:00:00 EST 2015 · Nature Communications

DOI:https://doi.org/10.1038/ncomms9898· OSTI ID:1229899

Baird, Nathan J. ^[1]; Inglese, James ^[1]; Ferré-D’Amaré, Adrian R. ^[1]

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1. National Inst. of Health (NIH), Bethesda, MD (United States)

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 MgCl₂, 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.

• Research Organization: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
• Sponsoring Organization: National Inst. of Health (NIH), Bethesda, MD (United States)
• OSTI ID: 1229899
• Journal Information: Nature Communications, Vol. 6, Issue 12; ISSN 2041-1723
• Publisher: Nature Publishing Group
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

biological sciences
biophysics
molecular biology