Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs

J Phys Chem B. 2009 Nov 26;113(47):15670-8. doi: 10.1021/jp906847p.

Abstract

We performed MP2 calculations to elucidate the structure and energetics of the Mg(2+), Mn(2+), and Co(2+) hexahydrated aquaions, and the effect of the metal binding to the N7 atom of (i) a single guanine, (ii) a guanine involved in a Watson-Crick pair, and (iii) a guanine involved in a reverse Watson-Crick base pair. Our comparative analysis of the three aquaions indicates a clear inverse correlation between the radius of the cation and the binding energy, that indeed increases in the order Mn(2+) < Co(2+) < Mg(2+). The trend in the binding energies of the pentahydrated cations to the N7 atom of the guanine is instead Mg(2+) < Mn(2+) < Co(2+), suggesting a rather different bonding scheme that, for the two transition metals, involves back-donation from the aromatic ring of the guanine to their empty d orbitals. In the gas phase, the three hydrated metals significantly stabilize both G-C base pair geometries, Watson-Crick and reverse Watson-Crick, we investigated. Inclusion of a continuous solvent model, however, remarkably reduces this additional stabilization, which becomes almost negligible in the case of the Mg(2+) cation coordinated to the guanine in the standard Watson-Crick geometry. Conversely, all three metal ions sensibly stabilize the reverse Watson-Crick geometry, also in water. Our results are supported by a screening of the structures available in the Protein Data Bank, which clearly indicates that the two transition metals we investigated have a tendency greater than Mg(2+) to coordinate to the N7 atom of guanines, and that there is no clear correlation between the number of guanines in experimental structures with a metal bound to N7 atom and their involvement in Watson-Crick base pairs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing*
  • Binding Sites
  • Cobalt / chemistry*
  • Guanine / chemistry*
  • Ions / chemistry*
  • Magnesium / chemistry*
  • Manganese / chemistry*
  • Molecular Conformation
  • Thermodynamics

Substances

  • Ions
  • Cobalt
  • Manganese
  • Guanine
  • Magnesium