Phosphoryl-Transfer Reaction in RNA under Alkaline Conditions

Carles Acosta-Silva, Joan Bertran, Vicenç Branchadell, Antoni Oliva

Research output: Contribution to journalArticleResearch

Abstract

© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim The phosphoryl-transfer reaction in RNA under alkaline conditions by exploring the influence of several solvents theoretically was studied. The calculations were carried out by using the M06-2X functional and the solvents were taken as a continuum by using the solvent model density (SMD) method. The main findings show that the O2′-P-O5′ angle in the reactants, the free activation energies, and the reaction mechanism are clearly dependent on the dielectric constant of the environment, thus showing that the electrostatic term is the determining factor for this chemical system with two negative charges. Our study seems to indicate that water, the solvent with the greatest dielectric constant, would be the solvent that increases the reaction rate the most. As this outcome was not the case in enzymatic catalysis, one has to conclude that, in the case of proteins as well as for ribozymes, the enzymatic catalysis is not mainly due to the solvent reaction field, but to local electrical fields as a result of enzyme preorganization.
Original languageEnglish
Pages (from-to)13565-13572
JournalChemistry - A European Journal
Volume24
Issue number51
DOIs
Publication statusPublished - 12 Sep 2018

Keywords

  • cleavage reactions
  • density functional calculations
  • enzyme catalysis
  • ribozymes
  • solvent reaction field

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