Analysis of actinomycin D-DNA model complexes using a quantum-chemical criterion: Mulliken overlap populations

J Mol Graph Model. 2005 Sep;24(1):10-6. doi: 10.1016/j.jmgm.2005.03.004.

Abstract

The binding of the antitumoral drug actinomycin D to single- and double-stranded DNA was investigated using molecular modeling in the frame of MM+ molecular mechanics and AM1 semi-empirical method. Two other programs, especially conceived to analyze hydrogen-bonding patterns in biological macromolecules, HBexplore, based on geometrical criteria and SHB_interactions, based on quantum-chemical criteria (Mulliken overlap populations), were also used. The results account for the non-cooperative intercalative binding process previously investigated, and outline the contribution of specific hydrogen bonding as well as CH...O(N) and other atom-atom intermolecular interactions to the stabilization of the actinomycin D-DNA complexes. They also support the hemi-intercalation model proposed in literature for the actinomycin D-ssDNA complex.

Publication types

  • Comparative Study

MeSH terms

  • DNA / chemistry*
  • DNA / metabolism
  • DNA, Z-Form / chemistry*
  • DNA, Z-Form / metabolism
  • Dactinomycin / chemistry*
  • Dactinomycin / metabolism
  • Hydrogen Bonding
  • Models, Chemical
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Quantum Theory*

Substances

  • DNA, Z-Form
  • Dactinomycin
  • DNA