ArticleRNA (New York, N.Y.)2010
Thermodynamic characterization of naturally occurring RNA tetraloops.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- Structure and sequence characteristics of 5'-stem-loop 1 modulate the escape from nsp1-mediated repression in SARS-CoV-2 variants.Nucleic acids research · 2026Article
- Latent thermodynamic flows: unified representation learning and generative modeling of temperature-dependent behaviors from limited data.Chemical science · 2026Article
- Structural basis and affinity improvement for an ATP-binding DNA aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Selective Nonenzymatic Formation of Biologically Common RNA Hairpins.Angewandte Chemie (International ed. in English) · 2025Article
- Inferring phase transitions and critical exponents from limited observations with thermodynamic maps.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- MeltR software provides facile determination of nucleic acid thermodynamics.Biophysical reports · 2023Article
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- Thermodynamic characterization of naturally occurring RNA pentaloops.RNA (New York, N.Y.) · 2022Article
- Rational design of hairpin RNA excited states reveals multi-step transitions.Nature communications · 2022Article
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.International journal of molecular sciences · 2021Article
- Article
- Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA.RNA (New York, N.Y.) · 2020Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Stability of RNA duplexes containing inosine·cytosine pairs.Nucleic acids research · 2018Article
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3 authors.
Funding
Abstract
Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters DeltaH degrees , DeltaS degrees , DeltaG degrees (37,) and T(M) for each stem-loop were determined. These new experimental values, on average, are 0.7 kcal/mol different from the values predicted for these tetraloops using the model proposed by Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Biochemistry 45: 1400-1407. The data for the 24 tetraloops reported here were then combined with the data for 28 tetraloops that were published previously. A new model, independent of terminal mismatch data, was derived to predict the free energy contribution of previously unmeasured tetraloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.4 kcal/mol. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem-loops containing tetraloops and, furthermore, should allow for improved prediction of secondary structure from sequence. It was also shown that tetraloops within the sequence 5'-GCCNNNNGGC-3' are, on average, 0.6 kcal/mol more stable than the same tetraloop within the sequence 5'-GGCNNNNGCC-3'. More systemic studies are required to determine the full extent of non-nearest-neighbor effects on tetraloop stability.
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