ArticleNucleic acids research2009
Classification and energetics of the base-phosphate interactions in 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 78 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
78 citing papers in PubMed, 173 citations in OpenAlex.
- R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.RNA (New York, N.Y.) · 2026Article
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Pseudouridine increases ribosome stability in a thermophilic eukaryote.Nucleic acids research · 2025Article
- The intrinsic preference of guanosine bases for cleavage-facilitating interactions with phosphodiester moieties in RNA anions revealed by base modifications and mass spectrometry.Nucleic acids research · 2025Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
- Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context.iScience · 2023Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- Occurrence and classification of T-shaped interactions between nucleobases in RNA structures.RNA (New York, N.Y.) · 2023Article
- Anionic G•U pairs in bacterial ribosomal rRNAs.RNA (New York, N.Y.) · 2023Article
- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs.Nucleic acids research · 2021Article
- Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study.Computational and structural biotechnology journal · 2021Article
- Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.Nucleic acids research · 2020Article
- Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.RNA (New York, N.Y.) · 2019Article
- The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.Nucleic acids research · 2019Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson-Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the 'Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.