DFT investigation of the mismatched base pairs (T-Hg-T)3, (U-Hg-U)3, d(T-Hg-T)2, and d(U-Hg-U)2

J Mol Model. 2014 Jun;20(6):2303. doi: 10.1007/s00894-014-2303-8. Epub 2014 May 31.

Abstract

Mismatched T:T and U:U base pairs in DNA and RNA duplexes represent the preferred target for mercury(II) cations. In this work, the structural, energetic, and electronic properties of the metallo base pairs T-Hg-T and U-Hg-U were investigated using density functional theory. In order to evaluate the geometric and energetic effects on the stacking interaction, the systems (T-Hg-T)3 and (U-Hg-U)3 systems as well as the dinucleotide systems d(T-Hg-T)2 and d(U-Hg-U)2 were examined. Results show that the exchange-correlation functionals B3LYP-D3 and M06-L yield reasonable information on these systems that is in agreement with the available experimental data.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pair Mismatch*
  • Base Pairing*
  • Computer Simulation*
  • Coordination Complexes / chemistry*
  • Energy Transfer
  • Models, Chemical*
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Organomercury Compounds / chemistry*
  • Structure-Activity Relationship
  • Uracil / chemistry*

Substances

  • Coordination Complexes
  • Organomercury Compounds
  • thymine-mercury(II)-thymine
  • Uracil