ArticleNucleic acids research2011
Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.Journal of chemical theory and computation · 2022Article
- A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.Nucleic acids research · 2021Article
- Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing.ACS applied materials & interfaces · 2021Article
- Perspective on the Future Role of Aptamers in Analytical Chemistry.Analytical chemistry · 2019Article
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.Chemical research in toxicology · 2017Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.Journal of the American Chemical Society · 2015Article
- Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.Biophysical journal · 2014Article
- Structure and mechanism of purine-binding riboswitches.Quarterly reviews of biophysics · 2012Review
- Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
6 authors.
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Abstract
Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch from Bacillus subtilis, for example, is stabilized by extensive interactions between apical loop regions of the aptamer domain. Previously, we have shown that destabilization of this tertiary loop-loop interaction abrogates ligand binding of the G37A/C61U-mutant aptamer domain (Gsw(loop)) in the absence of Mg(2+). However, if Mg(2+) is available, ligand-binding capability is restored by a population shift of the ground-state RNA ensemble toward RNA conformations with pre-formed loop-loop interactions. Here, we characterize the striking influence of long-range tertiary structure on RNA folding kinetics and on ligand-bound complex structure, both by X-ray crystallography and time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that the global architecture is almost identical to the wild-type aptamer domain. The population of ligand-binding competent conformations in the ground-state ensemble of Gsw(loop) is tunable through variation of the Mg(2+) concentration. We quantitatively describe the influence of distinct Mg(2+) concentrations on ligand-induced folding trajectories both by equilibrium and time-resolved NMR spectroscopy at single-residue resolution.
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