ArticleNucleic acids research2009
Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion.
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 10 papers.
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10 citing papers in PubMed, 33 citations in OpenAlex.
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- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- The Electronic Property Differences between dA::dG and dA::dGMolecules (Basel, Switzerland) · 2020Article
- The structural model of Zika virus RNA-dependent RNA polymerase in complex with RNA for rational design of novel nucleotide inhibitors.Scientific reports · 2018Article
- The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine.Nucleic acids research · 2017Article
- Visualizing single-stranded nucleic acids in solution.Nucleic acids research · 2017Article
- Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.The journal of physical chemistry. B · 2014Article
- Anomalies in the refinement of isoleucine.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.The journal of physical chemistry. A · 2013Article
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9 authors at 6 institutions in 4 countries.
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No grant is acknowledged in the PubMed record.
Abstract
We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides-it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.
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