ArticleNucleic acids research2015
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.Nature communications · 2026Article
- COCOMAPS 2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes.Bioinformatics (Oxford, England) · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- Viral condensates formed by Pea enation mosaic virus 2 sequester ribosomal components and suppress translation.Virology · 2025Article
- Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.Nucleic acids research · 2024Article
- Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The journal of physical chemistry. B · 2024Article
- RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators.Nature biotechnology · 2024Article
- Occurrence and classification of T-shaped interactions between nucleobases in RNA structures.RNA (New York, N.Y.) · 2023Article
- The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses.International journal of molecular sciences · 2023Review
- Translation ofFrontiers in molecular biosciences · 2023Review
- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Review
- The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function.RNA biology · 2022Review
- Article
- ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA.Journal of translational medicine · 2021Article
- The non-coding epitranscriptome in cancer.Briefings in functional genomics · 2021Review
- Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations.RNA (New York, N.Y.) · 2021Article
- Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study.Computational and structural biotechnology journal · 2021Article
- Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.Nucleic acids research · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. 'modified base pairs'. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson-Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.
Indexed as
Identifiers
What OpenQuestion holds
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.