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Angew Chem Int Ed Engl. 2016 Feb 18;55(8):2724-7. doi: 10.1002/anie.201509997. Epub 2016 Jan 21.

SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition.

Author information

1
Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
2
Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA. Dayie@umd.edu.

Abstract

Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.

KEYWORDS:

NMR spectroscopy; RNA; RNA dynamics; conformational dynamics; riboswitches

PMID:
26800479
DOI:
10.1002/anie.201509997
[Indexed for MEDLINE]

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