ArticleJournal of molecular biology2009
The influence of monovalent cation size on the stability of RNA tertiary structures.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Lithium in plants.The New phytologist · 2025Review
- GC Content and Thermal Stability of Double-Stranded RNA: Fragments of MicrosporidiaInternational journal of molecular sciences · 2025Article
- Structural basis of circularly permuted group II intron self-splicing.Nature structural & molecular biology · 2025Article
- Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs.RNA (New York, N.Y.) · 2024Article
- The RNA-binding Selectivity of the RGG/RG Motifs of hnRNP U is Abolished by Elements Within the C-terminal Intrinsically Disordered Region.Journal of molecular biology · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes.Scientific reports · 2022Article
- Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.Science advances · 2022Article
- An uncommon [KRNA (New York, N.Y.) · 2021Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Efficient depletion of ribosomal RNA for RNA sequencing in planarians.BMC genomics · 2019Article
- Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction.Nature communications · 2019Article
- Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix.Nucleic acids research · 2019Article
- Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies.The journal of physical chemistry. B · 2018Article
- Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.Journal of the American Chemical Society · 2017Article
- Reconstitution of a functional 7SK snRNP.Nucleic acids research · 2017Article
- Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding.Nucleic acids research · 2017Article
- The 2D Structure of theJournal of nucleic acids · 2017Article
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4 authors.
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Abstract
Many RNA tertiary structures are stable in the presence of monovalent ions alone. To evaluate the degree to which ions at or near the surfaces of such RNAs contribute to stability, the salt-dependent stability of a variety of RNA structures was measured with each of the five group I cations. The stability of hairpin secondary structures and a pseudoknot tertiary structure are insensitive to the ion identity, but the tertiary structures of two other RNAs, an adenine riboswitch and a kissing loop complex, become more stable by 2-3 kcal/mol as ion size decreases. This "default" trend is attributed to the ability of smaller ions to approach the RNA surface more closely. The degree of cation accumulation around the kissing loop complex was also inversely proportional to ion radius, perhaps because of the presence of sterically restricted pockets that can be accessed only by smaller ions. An RNA containing the tetraloop-receptor motif shows a strong (up to approximately 3 kcal/mol) preference for Na(+) or K(+) over other group I ions, consistent with the chelation of K(+) by this motif in some crystal structures. This RNA reverts to the default dependence on ion size when a base forming part of the chelation site is mutated. Lastly, an RNA aptamer for cobinamide, which was originally selected in the presence of high concentrations of LiCl, binds ligand more strongly in the presence of Li(+) than other monovalent ions. On the basis of these trends in RNA stability with group I ion size, it is argued that two features of RNA tertiary structures may promote strong interactions with ions at or near the RNA surface: negative charge densities that are higher than that in secondary structures, and the occasional presence of chelation sites, which are electronegative pockets that selectively bind ions of an optimum size.
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