ArticleNucleic acids research2020
Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
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- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Linker-Mediated Inactivation of the SAM-II Domain in the Tandem SAM-II/SAM-V Riboswitch.International journal of molecular sciences · 2024Article
- Full-Length NADBiochemistry · 2023Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.Nucleic acids research · 2023Article
- Discovering riboswitches: the past and the future.Trends in biochemical sciences · 2023Review
- Structure-based investigations of the NAD+-II riboswitch.Nucleic acids research · 2023Article
- Article
- The Biochemical Landscape of Riboswitch Ligands.Biochemistry · 2022Article
- Architectures and complex functions of tandem riboswitches.RNA biology · 2022Article
- Structure-based investigation of fluorogenic Pepper aptamer.Nature chemical biology · 2021Article
- Riboswitch Mechanisms: New Tricks for an Old Dog.Biochemistry. Biokhimiia · 2021Review
- Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.Nucleic acids research · 2021Article
- Impact of 3-deazapurine nucleobases on RNA properties.Nucleic acids research · 2021Article
- Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.Crystals · 2021Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD+. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD+ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg2+-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).
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