ArticleRNA (New York, N.Y.)2011
Non-nearest-neighbor dependence of the stability for RNA group II single-nucleotide bulge loops.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues.Frontiers in molecular biosciences · 2023Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A-U pairs in dsRNAs.Nucleic acids research · 2018Article
- Influence of two bulge loops on the stability of RNA duplexes.RNA (New York, N.Y.) · 2017Article
- Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine.RNA (New York, N.Y.) · 2015Article
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- Improved model to predict the free energy contribution of trinucleotide bulges to RNA duplex stability.Biochemistry · 2014Article
- Non-nearest-neighbor dependence of stability for group III RNA single nucleotide bulge loops.RNA (New York, N.Y.) · 2014Article
- Stability of single-nucleotide bulge loops embedded in a GAAA RNA hairpin stem.RNA (New York, N.Y.) · 2012Article
- Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops.Biochemistry · 2012Article
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9 authors.
Funding
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Abstract
Thirty-one RNA duplexes containing single-nucleotide bulge loops were optically melted in 1 M NaCl, and the thermodynamic parameters ΔH°, ΔS°, ΔG°(37), and T(M) for each sequence were determined. The bulge loops were of the group II variety, where the bulged nucleotide is identical to one of its nearest neighbors, leading to ambiguity as to the exact position of the bulge. The data were used to develop a model to predict the free energy of an RNA duplex containing a single-nucleotide bulge. The destabilization of the duplex by the bulge was primarily related to the stability of the stems adjacent to the bulge. Specifically, there was a direct correlation between the destabilization of the duplex and the stability of the less stable duplex stem. Since there is an ambiguity of the bulge position for group II bulges, several different stem combinations are possible. The destabilization of group II bulge loops is similar to the destabilization of group I bulge loops, if the second least stable stem is used to predict the influence of the group II bulge. In-line structure probing of the group II bulge loop embedded in a hairpin indicates that the bulged nucleotide is the one positioned farther from the hairpin loop.
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