ArticleBiochemistry2010
Thermodynamic characterization of RNA triloops.
Article in Biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- MeltR software provides facile determination of nucleic acid thermodynamics.Biophysical reports · 2023Article
- The Origin of Translation: Bridging the Nucleotides and Peptides.International journal of molecular sciences · 2022Review
- Thermodynamic characterization of naturally occurring RNA pentaloops.RNA (New York, N.Y.) · 2022Article
- Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.RNA (New York, N.Y.) · 2019Article
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- Blind prediction of noncanonical RNA structure at atomic accuracy.Science advances · 2018Article
- Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.PloS one · 2016Article
- Formation of Tertiary Interactions during rRNA GTPase Center Folding.Journal of molecular biology · 2015Article
- The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat.RNA biology · 2015Article
- Improved model to predict the free energy contribution of trinucleotide bulges to RNA duplex stability.Biochemistry · 2014Article
- Structural and thermodynamic signatures that define pseudotriloop RNA hairpins.RNA (New York, N.Y.) · 2013Article
- Effect of sodium ions on RNA duplex stability.Biochemistry · 2013Article
- Article
- Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.Biochemistry · 2012Article
- Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops.Biochemistry · 2012Article
- Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.Journal of molecular biology · 2011Article
- The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.FEBS letters · 2011Article
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Authors and funding
3 authors.
Funding
Abstract
Relatively few thermodynamic parameters are available for RNA triloops. Therefore, 24 stem-loop sequences containing naturally occurring triloops were optically melted, and the thermodynamic parameters ΔH°, ΔS°, ΔG°(37), and T(M) for each stem-loop were determined. These new experimental values, on average, are 0.5 kcal/mol different from the values predicted for these triloops using the model proposed by Mathews et al. [Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292]. The data for the 24 triloops reported here were then combined with the data for five triloops that were published previously. A new model was derived to predict the free energy contribution of previously unmeasured triloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.3 kcal/mol. These new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem-loops containing triloops and, furthermore, should allow for improved prediction of secondary structure from sequence.
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