{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kolev SK"],"funding":["Ministry of Education and Science","European Science Foundation","European Regional Development Fund"],"pagination":["23234-23244"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9280761"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["7(27)"],"pubmed_abstract":["The interactions between Na<sup>+</sup> or Mg<sup>2+</sup> ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg<sup>2+</sup> ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na<sup>+</sup> ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na<sup>+</sup> ions and 5.5 oxygen atoms for solvated Na<sup>+</sup> ions. In contrast, the inner solvation shell of Mg<sup>2+</sup> ions was stable in both RNA-bonded and completely solv"],"journal":["ACS omega"],"pubmed_title":["Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: <i>Ab Initio</i> Molecular Dynamics in Water Solution."],"pmcid":["PMC9280761"],"funding_grant_id":["D01-76/30.03.2021","BG05M2OP001-1.001- 0004 C01"],"pubmed_authors":["Milenov TI","Kolev SK","Vayssilov GN","St Petkov P"],"additional_accession":[]},"is_claimable":false,"name":"Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: <i>Ab Initio</i> Molecular Dynamics in Water Solution.","description":"The interactions between Na<sup>+</sup> or Mg<sup>2+</sup> ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg<sup>2+</sup> ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na<sup>+</sup> ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na<sup>+</sup> ions and 5.5 oxygen atoms for solvated Na<sup>+</sup> ions. In contrast, the inner solvation shell of Mg<sup>2+</sup> ions was stable in both RNA-bonded and completely solv","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Jul","modification":"2026-05-09T18:09:17.407Z","creation":"2022-07-19T09:20:55.139Z"},"accession":"S-EPMC9280761","cross_references":{"pubmed":["35847262"],"doi":["10.1021/acsomega.2c01327"]}}