A PM6 quantum chemical study of the H-bonded and stacked associates of the adenine and thymine DNA bases: The nature of base stacking

Victor I. Danilov, Tanja Van Mourik

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

Abstract

The planar H-bonded adenine-thymine (A center dot T) base pair and four stacked hetero associates (A/T) of these bases in a cluster containing 200 water molecules were studied by the new semi-empirical PM6 method. The formation of the planar A center dot T base pair in the water cluster was found to be energetically unfavourable, primarily due to the destabilising contribution of the base-water interactions. Under complete geometry optimisation, the planar A center dot T base pair converted into a nonplanar propeller-twisted and buckled associate. In contrast, the formation of all stacked dimers studied was found to be favourable, with formation energies ranging from -11 to -20 kcal/mol. The preference for the formation of these stacks results from the favourable change in the water structure and distortion of the paired and isolated bases during the base association reaction.

Original languageEnglish
Pages (from-to)1487-1494
Number of pages8
JournalMolecular Physics
Volume106
Issue number12-13
DOIs
Publication statusPublished - 2008

Keywords

  • adenine-thymine
  • base pair
  • base stacking
  • PM6
  • PLESSET PERTURBATION-THEORY
  • NUCLEIC-ACID BASES
  • MONTE-CARLO
  • FREE-ENERGY
  • DISPERSION FORCES
  • AROMATIC STACKING
  • AQUEOUS-SOLUTION
  • WATER SOLUTION
  • LOCAL MP2
  • APPROXIMATIONS

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