ArticleNucleic acids research2011
Tertiary contacts control switching of the SAM-I riboswitch.
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 32 papers.
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Who cites it
32 citing papers in PubMed, 49 citations in OpenAlex.
- Nucleotide-Resolution Mapping Reveals Specific MLE Binding Site on roX2 lncRNA.Journal of molecular biology · 2026Article
- Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.Communications biology · 2026Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth ofAntibiotics (Basel, Switzerland) · 2022Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.The journal of physical chemistry. B · 2021Article
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.Nature communications · 2020Article
- Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.Nucleic acids research · 2019Article
- Light-activated chemical probing of nucleobase solvent accessibility inside cells.Nature chemical biology · 2018Article
- Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.Nature chemical biology · 2017Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch.PLoS computational biology · 2017Article
- A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning.Journal of molecular biology · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Common themes and differences in SAM recognition among SAM riboswitches.Biochimica et biophysica acta · 2014Review
- Structure-guided design of fluorescent S-adenosylmethionine analogs for a high-throughput screen to target SAM-I riboswitch RNAs.Chemistry & biology · 2014Article
- Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are non-coding RNAs that control gene expression by sensing small molecules through changes in secondary structure. While secondary structure and ligand interactions are thought to control switching, the exact mechanism of control is unknown. Using a novel two-piece assay that competes the anti-terminator against the aptamer, we directly monitor the process of switching. We find that the stabilization of key tertiary contacts controls both aptamer domain collapse and the switching of the SAM-I riboswitch from the aptamer to the expression platform conformation. Our experiments demonstrate that SAM binding induces structural alterations that indirectly stabilize the aptamer domain, preventing switching toward the expression platform conformer. These results, combined with a variety of structural probing experiments performed in this study, show that the collapse and stabilization of the aptamer domain are cooperative, relying on the sum of key tertiary contacts and the bimodal stability of the kink-turn motif for function. Here, ligand binding serves to shift the equilibrium of aptamer domain structures from a more open toward a more stable collapsed form by stabilizing tertiary interactions. Our data show that the thermodynamic landscape for riboswitch operation is finely balanced to allow large conformational rearrangements to be controlled by small molecule interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.