ArticleNucleic acids research2007
The electrostatic characteristics of G.U wobble base pairs.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 48 citations in OpenAlex.
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- Precise in vivo RNA base editing with a wobble-enhanced circular CLUSTER guide RNA.Nature biotechnology · 2025Article
- A general strategy for engineering GU base pairs to facilitate RNA crystallization.Nucleic acids research · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- Molecular identification and phenotypic study of a novelFrontiers in medicine · 2025Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity.Nucleic acids research · 2021Article
- Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance.Nature communications · 2021Article
- Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With BaFrontiers in molecular biosciences · 2021Article
- Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.Chemical science · 2019Article
- New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants.RSC advances · 2018Article
- Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.Journal of computational chemistry · 2015Article
- An innate twist between Crick's wobble and Watson-Crick base pairs.RNA (New York, N.Y.) · 2013Review
- Progress in developing Poisson-Boltzmann equation solvers.Molecular based mathematical biology · 2013Article
- Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.Biochemistry · 2012Article
- The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.Biophysical journal · 2012Article
- The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.RNA (New York, N.Y.) · 2011Article
- Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication.ACS chemical biology · 2011Article
- A Fast and Robust Poisson-Boltzmann Solver Based on Adaptive Cartesian Grids.Journal of chemical theory and computation · 2011Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
G.U wobble base pairs are the most common and highly conserved non-Watson-Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G.U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson-Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G.U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G.U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G.U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G.U sites in RNA are most likely to bind cationic ligands.
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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.