ArticleNucleic acids research2009
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Periodic Temperature Fluctuations as an Energy Source for RNA Evolution.Life (Basel, Switzerland) · 2026Article
- Thermodynamic determination of RNA duplex stability in magnesium solutions.Biophysical journal · 2023Article
- A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including NJournal of molecular biology · 2022Article
- A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs.RNA biology · 2020Article
- Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions.Nucleic acids research · 2019Article
- Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.Biochemistry · 2019Article
- Stability of RNA duplexes containing inosine·cytosine pairs.Nucleic acids research · 2018Article
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.Biochemistry · 2018Article
- Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.RNA (New York, N.Y.) · 2017Article
- Enhancing potency of siRNA targeting fusion genes by optimization outside of target sequence.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Effect of sodium ions on RNA duplex stability.Biochemistry · 2013Article
- Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.Biochemistry · 2012Article
- Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches.Biochemistry · 2010Article
- RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.Biochemistry · 2010Article
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Authors and funding
2 authors.
Funding
Abstract
Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329-4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence.
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