ArticleNucleic acids research2006
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 58 citations in OpenAlex.
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- A general strategy for engineering GU base pairs to facilitate RNA crystallization.Nucleic acids research · 2025Article
- Anionic G•U pairs in bacterial ribosomal rRNAs.RNA (New York, N.Y.) · 2023Article
- Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field.Journal of chemical theory and computation · 2022Article
- Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures.Nucleic acids research · 2022Article
- Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.Nucleic acids research · 2020Article
- Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2.RNA (New York, N.Y.) · 2020Article
- The multiple flavors of GoU pairs in RNA.Journal of molecular recognition : JMR · 2019Review
- How to fold and protect mitochondrial ribosomal RNA with fewer guanines.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.Nucleic acids research · 2015Article
- Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Physical chemistry chemical physics : PCCP · 2015Article
- Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- RNA modularity for synthetic biology.F1000prime reports · 2013Review
- The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns.Journal of molecular biology · 2012Article
- The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.RNA (New York, N.Y.) · 2011Article
- A close-up view on ITS2 evolution and speciation - a case study in the Ulvophyceae (Chlorophyta, Viridiplantae).BMC evolutionary biology · 2011Article
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket--like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)--lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved through a series of compensatory mutations involving all four participating nucleotides to preserve or restore the G/U in the optimal orientation. Second, a G/U basepair forming a P-interaction and another one forming a phosphate-in-pocket interaction are replaced by GNRA loops that maintain similar tertiary contacts. MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments.
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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.