ArticleRNA (New York, N.Y.)2008
Thermodynamic examination of trinucleotide bulged RNA in the context of HIV-1 TAR RNA.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 17 citations in OpenAlex.
- Solid-Phase Synthesis Approaches and U-Rich RNA-Binding Activity of Homotrimer Nucleopeptide Containing Adenine Linked toInternational journal of molecular sciences · 2025Article
- Solid Phase Synthesis and TAR RNA-Binding Activity of Nucleopeptides Containing Nucleobases Linked to the Side Chains via 1,4-Linked-1,2,3-triazole.Biomedicines · 2024Article
- Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop.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
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs.RNA (New York, N.Y.) · 2015Article
- Improved model to predict the free energy contribution of trinucleotide bulges to RNA duplex stability.Biochemistry · 2014Article
- Quantifying the temperature dependence of glycine-betaine RNA duplex destabilization.Biochemistry · 2013Article
- Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch.RNA (New York, N.Y.) · 2011Article
- Non-enzymatic template-directed recombination of RNAs.International journal of molecular sciences · 2009Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA structures contain many bulges and loops that are expected to be sites for inter- and intra-molecular interactions. Nucleotides in the bulge are expected to influence the structure and recognition of RNA. The same stability is assigned to all trinucleotide bulged RNA in the current secondary structure prediction models. In this study thermal denaturation experiments were performed on four trinucleotide bulged RNA, in the context of HIV-1 TAR RNA, to determine whether the bulge sequence affects RNA stability and its divalent ion interactions. Cytosine-rich bulged RNA were more stable than uracil-rich bulged RNA in 1 M KCl. Interactions of divalent ions were more favorable with uracil-rich bulged RNA by approximately 2 kcal/mol over cytosine-rich bulged RNA. The UCU-TAR RNA (wild type) is stabilized by 1.7 kcal/mol in 9.5 mM Ca(2+) as compared with 1 M KCl, whereas no additional gain in stability is measured for CCC-TAR RNA. These results have implications for base substitution experiments traditionally employed to identify metal ion binding sites. To our knowledge, this is the first systematic study to quantify the effect of small sequence changes on RNA stability upon interactions with divalent ions.
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